RetrogeneDB

RetrogeneDB ID:
retro_ecab_1063
Organism:
Horse ( Equus_caballus )
Location:
X:42841867-42843322 (+)
Status:
KNOWN_PSEUDOGENE
Ensembl ID:
ENSECAG00000017595
Aliases:
No gene alias available
Located in intron of:
None
Alignment summary

Identity:
77.87 %
Coverage:
82.96 %
Frameshifts:
0
Stop codons:
0


Parental gene:
ENSECAG00000019110
Parental gene symbol:
UBQLN1
Parental gene aliases:
No gene alias available
Parental gene description:
ubiquilin 1 [Source:HGNC Symbol;Acc:12508]

Genomic region (view in browser)





>retro_ecab_1063
ATGGCTGAGAACGGCGAGAGCAGCGGCCCCCCGCGCCCCTCCCGTGGCCCTGCTTCGGCC
CAAGGCCCTGCCTCTGCTCCGGCCGAGCCCAAAATCATCAAAGTCACTGTGAAGACCCCC
AAAGAGAAAGAGGAGTTCGCGGTGCCCGAGAATAGCTCAGTCCAGCAGTTTAAGGAAGCG
ATTTCGAAACGCTTCAAATCCCAAACCGATCAGCTAGTGCTGATTTTTGCCGGAAAAATC
TTAAAAGATCAAGATACCTTGATCCAGCACGGCATCCATGATGGACTGACTGTTCACCTT
GTCATCAAAAGCCAGAACCGACCTCAGGGCCAGTCCACACAGCCTAGTAATGCCGCGGGA
ACTAATACTACCTCCCCGTCGACTCCCAGGAATAACTCCACACCTCTTTCCACAAATAGC
AACCCATTTGGTTTGGGGAGCCTGGGAGGACTTGCAGGCCTTAGCAGCCTGGGCTTGAGC
TCAACCAACTTCTCTGAGCTCCAGAACCAGATGCAGCAGCAGCTCCTGTCCAGCCCTGAG
ATGATGATCCAAATCATGGAAAATCCCTTTGTTCAGAGCATGCTTTCGAATCCTGATCTA
ATGAGGCAGCTCATTATGGCCAATCCACAGATGCAACAGTTGATTCAGAGAAACCCAGAA
ATCAGTCACCTGCTCAACAACCCAGATATAATGAGGCAGACCCTGGAAATAGCCAGGAAT
CCAGCCATGATGCAAGAGATGATGAGAAATCAGGACCTGGCTCTCAGCAATCTCGAAAGC
ATCCCAGGTGGCTACAATGCCCTGCGGCGCATGTACACTGACATTCAAGAACCCATGCTG
AATGCCGCACAAGAGCAGTTTGGGGGTAATCCATTTGCCTCGGTGGGGAGCAGTTCTTCC
TCTGGGGAAGGCACGCAGCCTTCTCGCACAGAAAATCGAGATCCACTACCCAATCCATGG
GCACCACCACCGGCTACCCAGAGTTCTGCGACCACCAGCACAACCTCAAGCAGTGGCAGT
GGCAGTGGCAGTGGGTCTGGTAGTAGCTCCACCAGTGCTACCGGGAACACCGTGGCTGCA
GCCAATTATGTTGCCAGCATCTTCAGTACCCCAGGAATGCAGAGCTTACTGCAACAGATA
ACTGAAAACCCCCAGCTGATCCAGAATATGCTGTCTGCGCCCTACATGAGAAGCATGATG
CAGTCGCTGAGCCAGAATCCAGATTTGGCTGCACAGATGATGCTGAATAGCCCCGTGTTT
ACTGCAAATCCTCAGCTGCAGGAGCAGATGCGTCCCCAGCTCCCGGCTTTCCTACAGCAG
ATGCAGAATCCAGACACACTCTCAGCTATGTCAAACCCAAGAGCAATGCAGGCTTTAATG
CAGATCCAGCAGGGGCTACAGACATTAGCCACTGAAGCACCTGGCCTCATTCCAAGCTTC
GCTCCAGGTGTAGGG

Library Expression (reads per million mapped reads)
SRP021940_articular_cartilage 20.62
SRP021940_cerebellum 100.42
SRP021940_embryo 59.63
SRP021940_placental_villous 9.66
SRP021940_synovial_membrane 19.25
SRP021940_testis 2.85

Parental protein coverage





Changes in the retrocopy sequence






Parental protein
MAENSESGGPPSSQDSAAAAEGAGATAAASAEPKIMKVTVKTPK-KEDFAVPENSSVQQFKEEISKRFKSHTDQLVLIFAGKILKDQDTLSQHGIHDGLT
MAEN.ES.GPP......A.A.G....A.A.AEPKI.KVTVKTPK.KE.FAVPENSSVQQFKE.ISKRFKS.TDQLVLIFAGKILKDQDTL.QHGIHDGLT
Retrocopy
MAENGESSGPPRPSRGPASAQGP---ASAPAEPKIIKVTVKTPKEKEEFAVPENSSVQQFKEAISKRFKSQTDQLVLIFAGKILKDQDTLIQHGIHDGLT


Parental protein
VHLVIKTQNRPQDHSAQQTNTSGSGVTTSSAPNSNSTSGSATSNPFGLGGLGGLAGLSSLGLNTTNFSELQSQMQRQLMSNPEMMVQIMENPFVQSMLSN
VHLVIK.QNRPQ..S.Q..N..G...T..S.P..NST..S..SNPFGLG.LGGLAGLSSLGL..TNFSELQ.QMQ.QL.S.PEMM.QIMENPFVQSMLSN
Retrocopy
VHLVIKSQNRPQGQSTQPSNAAGTNTTSPSTPRNNSTPLSTNSNPFGLGSLGGLAGLSSLGLSSTNFSELQNQMQQQLLSSPEMMIQIMENPFVQSMLSN


Parental protein
PDLMRQLIMANPQMQQLIQRNPEISHMLNNPDIMRQTLELARNPAMMQEMMRNQDRALSNLESIPGGYNALRRMYTDIQEPMLSAAQEQFGGNPFASLVS
PDLMRQLIMANPQMQQLIQRNPEISH.LNNPDIMRQTLE.ARNPAMMQEMMRNQD.ALSNLESIPGGYNALRRMYTDIQEPML.AAQEQFGGNPFAS..S
Retrocopy
PDLMRQLIMANPQMQQLIQRNPEISHLLNNPDIMRQTLEIARNPAMMQEMMRNQDLALSNLESIPGGYNALRRMYTDIQEPMLNAAQEQFGGNPFASVGS


Parental protein
STSSGEGSQPSRTENRDPLPNPWAPQASQGSSASGGTASAVGGTGGSAASGTAGQSSTAPNLGPGVGASMFNTPGMQSLLQQITENPQLMQNMLSAPYMR
S.SSGEG.QPSRTENRDPLPNPWAP.....SSA...T.S............................AS.F.TPGMQSLLQQITENPQL.QNMLSAPYMR
Retrocopy
SSSSGEGTQPSRTENRDPLPNPWAPPPATQSSATTSTTSXXXXXXXXXSGSSSTSATGNTVAAANYVASIFSTPGMQSLLQQITENPQLIQNMLSAPYMR


Parental protein
SMMQSLSQNPDLAAQMMLNNPLFAGNPQLQEQMRQQLPTFLQQMQNPDTLSAMSNPRAMQALLQIQQGLQTLATEAPGLIPGFTPGLG
SMMQSLSQNPDLAAQMMLN.P.F..NPQLQEQMR.QLP.FLQQMQNPDTLSAMSNPRAMQAL.QIQQGLQTLATEAPGLIP.F.PG.G
Retrocopy
SMMQSLSQNPDLAAQMMLNSPVFTANPQLQEQMRPQLPAFLQQMQNPDTLSAMSNPRAMQALMQIQQGLQTLATEAPGLIPSFAPGVG


Legend:
*
Stop codon
\
Forward frameshift by one nucleotide
/
Reverse frameshift by one nucleotide






stat4u