RetrogeneDB ID: retro_ocun_1020

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 19:27098624..27099757(-)
• Located in intron of: ENSOCUG00000010794

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSOCUG00000010375
• Aliases: None
• Description: Eukaryotic initiation factor 4A-I [Source:UniProtKB/Swiss-Prot;Acc:P29562]

Sequence

>retro_ocun_1020
AACAGATCCAGAGACAATGGCCCCTATGGGATAGAGCCCTAAGGTATCATCAAGAGTAACTGAAGTGAAGACCATTGACA
GCTTTGATGACATGAACCTCTCTGAGTCCCTCCTTCATGGCATCTACGCCTATGGTTTTCAGAAGCACTCTGCCATCCAG
CAGCATGCCATTCTGCCTTGTAGCAAGGGTTATAATGGGATTGCTCAAGCCCAATCTGGGACTTGGAAAATGGCCACATT
TGCCATATCAATTCTACAGCAGATTGAATTGGATCTGAAGGCCACCCAGGCCTAGGTACTAGCATCCACACAGGAATTGG
CCCAACAGATACAAAAGGTGGTCATGACATTAGGAGATTACATGGGTGCATCCTGTCACACCTGCACTGGGGGCACCAAC
GTTCATGCTGAGCTGCAGAAACTGCAAATGGAAGTTCCTCATATCATTGTGGGCACCCCTGGCCACTTATTCGACATGCT
TAACTGGAGATACCTGTCTCCCAAATACATCAAGATGTCTGTACTGGATGAAGCTGATGAAATGTTAAGCCGTGGATTCA
AGGAACAGATCTATGACATCTTCTAAAAGCTCAACAGCAGCACCAGGTGGTTTTGCTGTCAGCTACAATGCCTTCCGATG
TGTTCGAGGTGACCAAGAAGTTCACGGGGGACCCCATCTGGATTCTTGACAAGAAGGAAGAGTTGACCCTGGAGGATATC
TGCCAGTTCTACATCAACGTGGAACGCAAGGAGTGGAAGCTGGACACACTGTGTGGCTTGTGTGAAACCCTGACCATAAC
CCAGCCTGTCGTCTTCATCAATACCCGAAGGAATGTCAAGAAGCTCACTGAGAAGATGCACGCCCAGACCTCACTGTCTC
TGCCATGCTTGGAGATACGGAGCAAAAGGAGTGCGATGCGAGCATGAGGGAGTTCCGTTCTGGCTCTAGCCGAGTACTGA
TTACCACTGACCTGCTGGCCAGAGGCATTGATGTGCAACAGGTTTCTGCAGTCATCAACTATGACCTTCCCACTGACAGG
GAAAACTATATTCACAGAACTGGCCACAGTGGGCGTTTTGGTTGTAAGAGAGTGGCTATTAACAAGGTGACAGAAGACAG
GCAGACTCTTAGA

Alignment

ORF - retro_ocun_1020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.15 %
• Parental protein coverage: 93.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRSRDNGPDGMEPEGVIESNWNE-IVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQ
          .RSRDNGP.G.EP.G.I.SN..E...DSFDDMNLSESLL.GIYAYGF.K.SAIQQ.AILPC.KGY..IAQ
Retrocopy NRSRDNGPYGIEP*GIIKSN*SE>TIDSFDDMNLSESLLHGIYAYGFQKHSAIQQHAILPCSKGYNGIAQ

Parental  AQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQ
          AQSGT.K.ATFAISILQQIELDLKATQA.VLA.T.ELAQQIQKVVM.LGDYMGASCH.C.GGTNV.AE.Q
Retrocopy AQSGTWKMATFAISILQQIELDLKATQA*VLASTQELAQQIQKVVMTLGDYMGASCHTCTGGTNVHAELQ

Parental  KLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNT-QVVLLSA
          KLQME.PHIIVGTPG..FDMLN.RYLSPKYIKM.VLDEADEMLSRGFK.QIYDIF.KLNS.T.QVVLLSA
Retrocopy KLQMEVPHIIVGTPGHLFDMLNWRYLSPKYIKMSVLDEADEMLSRGFKEQIYDIF*KLNSST<QVVLLSA

Parental  TMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRK
          TMPSDV.EVTKKF..DPI.IL.KKEELTLE.I.QFYINVER.EWKLDTLC.L.ETLTITQ.V.FINTRR.
Retrocopy TMPSDVFEVTKKFTGDPIWILDKKEELTLEDICQFYINVERKEWKLDTLCGLCETLTITQPVVFINTRRN

Parental  VDWLTEKMHAR-DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNR
          V..LTEKMHA..D.TVSAM.GD..QKE.D..MREFRSGSSRVLITTDLLARGIDVQQVS.VINYDLPT.R
Retrocopy VKKLTEKMHAQ<DLTVSAMLGDTEQKECDASMREFRSGSSRVLITTDLLARGIDVQQVSAVINYDLPTDR

Parental  ENYIHRIGRGGRFGRKGVAINMVTEEDKRTLR
          ENYIHR.G..GRFG.K.VAIN.VT.ED..TLR
Retrocopy ENYIHRTGHSGRFGCKRVAINKVT-EDRQTLR

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	85.60 RPM
SRP017611_kidney	0.00 RPM	143.12 RPM
SRP017611_liver	0.00 RPM	73.91 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1020 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1020 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1020 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000132	1 retrocopy	retro_btau_1207,
Loxodonta africana	ENSLAFG00000001107	1 retrocopy	retro_lafr_1210,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Oryctolagus cuniculus	ENSOCUG00000005011	3 retrocopies	retro_ocun_392, retro_ocun_696, retro_ocun_763,
Oryctolagus cuniculus	ENSOCUG00000010375	5 retrocopies	retro_ocun_1020 , retro_ocun_1326, retro_ocun_1375, retro_ocun_475, retro_ocun_934,
Pongo abelii	ENSPPYG00000007926	7 retrocopies	retro_pabe_1090, retro_pabe_1474, retro_pabe_3759, retro_pabe_3792, retro_pabe_548, retro_pabe_846, retro_pabe_987,