RetrogeneDB ID: retro_ocun_929

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:6479289..6480428(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000010064
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010667
• Aliases: None
• Description: None

Sequence

>retro_ocun_929
ATGTTGTCATCCGTGTACGCCTGGTCCCCACGACAGTCCGGCTAGTCCATTCTCTGAACTGCATTTCTTCCTGTTCCTTC
ATGGACCTGAAGACTCTCATCTCCTCCTTGAATGACTTTGCCTCCCTATCTTTTGCTGAGAGTTGGGACAATGTTGGATT
GCGGGTAGAACCACGCCCGCCACATACTGTGAATACACCCTTCCTGACCAATGACTCAACTGGAGATGATGATGGAGGTG
ATGGAGGAGGCTCTGCATAAGAAGGCAGATCTCATCCATGCCTTCCATCCACCCATCTTCCTACCCGTAAAGCGTACAAC
CTGGAAGTCCTGGAACGAGCGCCTGGTGATTCGGGCTTTGGAAAACAGAGTCGCCGTCTACTTTCCTCCCACAGCCTATG
ACACTGCACCCCAGGGAGTGAACAACTGGTTGTCCAAAGGGCTTGGAGCCCGCACATGCAGGCCCATATGGCCTTCCAAA
GCTCACAGCTGTCCTACAGAGGGAACCCACCGGAGAGAATTCAACATTAACCATACCCAAGCTCTGGACAAAGTCGTGTC
TGCAGTGAGAGAAATCGAAGGTGTTTCTGTCACTTCTTTTTCTGCTCGGATTGGTGATGAGGAACAAACACGGATCAGCC
TGGATTGTACTGAGAAGGCGTTGATGCAGGGGATGGCTCAGCTCTCCGAAAACGGACAACTTTGTCAGAGAGCTGGAATT
CTGTCGCTGGAGAAGCCTTTGCCTCTACACACTGGAATGGGACAGTTATGCACTATGGATGAATCTGTTTCCCTGGCAAC
CATGATTGAGCAAATCAAAAGACATCTCCAGCTAACTCGTATTCGCTTAGCTCTTGGGGTGGAAAGGACCTCAGAGTCGC
GGGCCGGAGCTGTGGCCCTGTGTGCTGGTTCTGGGAGCAGCGTCCTGCGGGGTGTGGAAGCTGACCTTCACCTCACAGGT
GAGATGTCCCCTCGTGATGCTCCGATGCTACCTCCTGAGGAGTCAATGTCATCGTCTGTGAACACAGTAACACGGAATGA
GGCTTCCTTTCTGACCTTCGTAATACGCTGGGTGCCCACTTGGAGAATAAGATTAATATTATCCTGTCGGAGACAGACAG
GGATCCTCTGCGTGTGGTG

Alignment

ORF - retro_ocun_929 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLSSC-ARLAPSTVRLVHSLDCSSSRSFMDLKALISSLNDFASLSFAESWDNVGLLVEPSPPHTVNTLFL
          MLSS...RL.P.TVRLVHSL.C.SS.SFMDLK.LISSLNDFASLSFAESWDNVGL.VEP.PPHTVNT.FL
Retrocopy MLSSV<VRLVPTTVRLVHSLNCISSCSFMDLKTLISSLNDFASLSFAESWDNVGLRVEPRPPHTVNTPFL

Parental  TNDLT-EPVME---EALQKKADLILSYHPPIFLPMKRITWKSWKERLVIRALENRVAIYSPHTAYDAAPQ
          TND.T.E..ME...EAL.KKADLI...HPPIFLP.KR.TWKSW.ERLVIRALENRVA.Y.P.TAYD.APQ
Retrocopy TNDST>EMMMEVMEEALHKKADLIHAFHPPIFLPVKRTTWKSWNERLVIRALENRVAVYFPPTAYDTAPQ

Parental  GVNNWLSKGLGACTSRPICPSKAHSYPTEGTHRVEFNVNHTQDLDKVVSAVREIEGVSVTSFSARTDGEE
          GVNNWLSKGLGA.T.RPI.PSKAHS.PTEGTHR.EFN.NHTQ.LDKVVSAVREIEGVSVTSFSAR...EE
Retrocopy GVNNWLSKGLGARTCRPIWPSKAHSCPTEGTHRREFNINHTQALDKVVSAVREIEGVSVTSFSARIGDEE

Parental  QTRISLNCTEKALMQVVAQLSQNRQLYQRTEILSLEKPLLLHTGMGRLCTLDESVSLATMIERIKRHLKL
          QTRISL.CTEKALMQ..AQLS.N.QL.QR..ILSLEKPL.LHTGMG.LCT.DESVSLATMIE.IKRHL.L
Retrocopy QTRISLDCTEKALMQGMAQLSENGQLCQRAGILSLEKPLPLHTGMGQLCTMDESVSLATMIEQIKRHLQL

Parental  THIRLALGVERTLESRVEVVALCAGSGSSVLRGVEADLYLTGEMSHHDV-LDATSRGISVILCEHSNTER
          T.IRLALGVERT.ESR...VALCAGSGSSVLRGVEADL.LTGEMS..D...DATS.G..VI.CEHSNTE.
Retrocopy TRIRLALGVERTSESRAGAVALCAGSGSSVLRGVEADLHLTGEMSPRDA<SDATS*GVNVIVCEHSNTE*

Parental  GFLSDLRDMLGVHLENRIHIVLSETDRDPLCVV
          GFLSDLR..LG.HLEN.I.I.LSETDRDPL.VV
Retrocopy GFLSDLRNTLGAHLENKINIILSETDRDPLRVV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	9.99 RPM
SRP017611_kidney	0.00 RPM	15.71 RPM
SRP017611_liver	0.00 RPM	5.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_929 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_929 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_929 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023186	1 retrocopy	retro_fcat_589,
Macaca mulatta	ENSMMUG00000006639	1 retrocopy	retro_mmul_444,
Nomascus leucogenys	ENSNLEG00000006935	1 retrocopy	retro_nleu_1504,
Oryctolagus cuniculus	ENSOCUG00000010667	16 retrocopies	retro_ocun_1105, retro_ocun_1534, retro_ocun_1539, retro_ocun_1691, retro_ocun_1692, retro_ocun_1710, retro_ocun_1729, retro_ocun_1749, retro_ocun_1789, retro_ocun_1828, retro_ocun_1837, retro_ocun_1841, retro_ocun_1846, retro_ocun_1847, retro_ocun_1854, retro_ocun_929 ,
Pongo abelii	ENSPPYG00000013063	1 retrocopy	retro_pabe_244,
Tupaia belangeri	ENSTBEG00000000704	1 retrocopy	retro_tbel_3512,