RetrogeneDB ID: retro_ocun_1089

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:32301207..32302006(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: AP1M2
• Ensembl ID: ENSOCUG00000024334
• Aliases: None
• Description: adaptor-related protein complex 1, mu 2 subunit [Source:HGNC Symbol;Acc:558]

Sequence

>retro_ocun_1089
GTGGAGATCTGCTGCAAATACTTCAAGGAGCTGGAGGAGGAGAGCATCCATGATAGCTATGAGCTATTGGATGAACTCAT
GGACTTCAGCTTTCCCCAGACCACTGACAGCAAGATCCTGTAGGAGTGTATAATGCAACAGGACAACAGGCTGGAGACCA
GCAAGTCGCTGGTGCTGCCCACTGTCACCAATGCTGTGTCTTAATGCTCTGAGGGCAACAAGGACAAGAAAAAGAGGTCT
TCATCGACATCATTGAGTCTGTCAACCCGTCGGTCAATGCCAATGGCAGCCTGATGCTCAGGAAGATTGTGGGCACAGTC
AAGCTCAAGGTGTTTCTGTCAGGCATGCTGGAGCTGCAGCCCAGTCTCAATAACCAACTACTGTTCGAGCTCACTGGCCT
TTCAGGAAGCAAAAACAAGTCCGTGGAGCTGGGGGACATGAAGTTCCACCAGTGTACACAGCTCTCTCACTTAGACAGTG
ACTGTAACCATCTCCTTCTCCTCTCTGGATGGTCACTTTGAGCTCATGCCCTACCGTTTTCACAGCCAGGTCAAACCTCT
GATCTGGATCAAGTCTGTCATTGAGAAGTTTTCTCAGAGCCATGTGGAGATCATGGTCAAGGCCAAGGGCCAGTTTAAGA
AGCAGTTGGTAGCCAACAGTATGGAGATCTCTGTGCCCGCTCCAGCGATGCAGACCCCCCCCATGCTTCAAGATCAACAT
GGGCAGTGCCAAGTCTGTTCCAAAGAAGAATGTGATCATTTAGAGCATCAAGTCCTTCCCAGGTGGCAAGCCATACCTG

Alignment

ORF - retro_ocun_1089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.8 %
• Parental protein coverage: 62.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VEVGTEYIYSLDERRMITVGSLLDELMDFGFPQTTDSKILQEYITQQGNKLETGKSRVPPTVTNAVSWRS
          VE....Y...L.E........LLDELMDF.FPQTTDSKIL.E.I.QQ.N.LET.KS.V.PTVTNAVS..S
Retrocopy VEICCKYFKELEEESIHDSYELLDELMDFSFPQTTDSKIL*ECIMQQDNRLETSKSLVLPTVTNAVS*CS

Parental  EGIKYKKN-EVFIDVVESVNLLVNAN-SVLLSEIVGTIKLKVFLSGMPE-RLGLNDRVLFELTGRS--KS
          EG.K.KK..EVFID..ESVN..VNAN.S..L..IVGT.KLKVFLSGM.E....LN...LFELTG.S..K.
Retrocopy EGNKDKKK<EVFIDIIESVNPSVNANGSLMLRKIVGTVKLKVFLSGMLELQPSLNNQLLFELTGLSGSKN

Parental  KSVELEDVKFHQCVRLSRFDNDR-TISFIPPDGDFELMSYRLNTQVKPLIWIESVIEKFSHSRVEIMVKA
          KSVEL.D.KFHQC..LS..D.D..TISF...DG.FELM.YR...QVKPLIWI.SVIEKFS.S.VEIMVKA
Retrocopy KSVELGDMKFHQCTQLSHLDSDC>TISFSSLDGHFELMPYRFHSQVKPLIWIKSVIEKFSQSHVEIMVKA

Parental  KGQFKKQSVANGVEISVPVPSDADSPR-FKTSVGSAKYVPEKNVVIWSIKSFPGGKEYL
          KGQFKKQ.VAN..EISVP.P.....P..FK...GSAK.VP.KNV.I.SIKSFPGGK.YL
Retrocopy KGQFKKQLVANSMEISVPAPAMQTPPM>FKINMGSAKSVPKKNVII*SIKSFPGGKPYL

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	0.28 RPM
SRP017611_kidney	0.00 RPM	20.47 RPM
SRP017611_liver	0.00 RPM	0.69 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1089 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1089 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000003643	1 retrocopy	retro_meug_1894,
Monodelphis domestica	ENSMODG00000005838	2 retrocopies	retro_mdom_1571, retro_mdom_451,
Ornithorhynchus anatinus	ENSOANG00000010455	1 retrocopy	retro_oana_88,
Oryctolagus cuniculus	ENSOCUG00000004556	1 retrocopy	retro_ocun_98,
Oryctolagus cuniculus	ENSOCUG00000024334	1 retrocopy	retro_ocun_1089 ,