RetrogeneDB ID: retro_ocun_1326

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:123062094..123062962(+)
• Located in intron of: ENSOCUG00000013133

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_1326
CAAATACAAAAGGTGGTCATGGCATTAGGATTTTACATGGGTGCATCCTGTCACACCTGCACTGGGAGCACCAATGTGTG
TGCTGAGGTGCAGAAACTGCAAATGGAAGCTCCCCATATTATTGTGGGCACCCCTGGCCACGTATTCGACATGCTTAGCT
AAAGATACCTGTCTCCCAAATACATCAAGATGTTTGTACTGGACGAAGCTGATGAAATGTTAAGCCATGGATTCAAGGAC
CAGATCTATGACATCTTCCAAAAGCTCAACCGCAACACCAGGTGGTTTTGTTGTCAGCTACAATGCTTTTCAATGTGCTT
GAAGGGATCAAGAAGTTGATGAGGGATCCTATCCGGATTCTTGTCAAGAAGGAAAAGCTGACCCTGGAGGGTATCCGCCA
GTTCTACATCAACAGAGAAGGCAAGGAGTAGAAGGTGGACACACTGAGTGACTTGTACGAAATGCTGAGCATAACCCAGG
CTGTCATCTTCATCAATACCCGAAGGAAGGTCAATTGGCTCACTCAGAAGATGCATGCCCGGGACTTCACTGTTACGCAT
GGAGATATGGACCAAAAGGAGCAAGATATGATCATGAGGGAGTTCCATTATGGCTCTAGCCAAGCACTGATTACCACTGA
CCTGCTGGCTAGAGGTGTTGATGTATAGCAAGTTTCTTTGGTCATCAACTATGACCTACCCACCAACAGAGAAATCTATA
TTCACAGAATTGGCCATGGTGGATGTTTTGGTCATAAGGGTTTGGCTATTAACAGGGTGACAGGAGAAGACAAGCAGACT
CTTCAAGACATCAGACCTTCTACAACACCTCCATTGAGGAGATGCCCCTCAATGTTGCCGACCTCATC

Alignment

ORF - retro_ocun_1326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.99 %
• Parental protein coverage: 71.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEA
          QIQKVVMALG.YMGASCH.C.G.TNV.AEVQKLQMEAPHIIVGTPG.VFDML..RYLSPKYIKMFVLDEA
Retrocopy QIQKVVMALGFYMGASCHTCTGSTNVCAEVQKLQMEAPHIIVGTPGHVFDMLS*RYLSPKYIKMFVLDEA

Parental  DEMLSRGFKDQIYDIFQKLNSNT-QVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINV
          DEMLS.GFKDQIYDIFQKLN.NT.QVVLLSATM...VLE..KK.MRDPIRILVKKE.LTLEGIRQFYIN.
Retrocopy DEMLSHGFKDQIYDIFQKLNRNT<QVVLLSATMLFNVLEGIKKLMRDPIRILVKKEKLTLEGIRQFYINR

Parental  EREEWKLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSS
          E..E.K.DTL.DLYE.L.ITQAVIFINTRRKV.WLT.KMHARDFTV...HGDMDQKE.D.IMREF..GSS
Retrocopy EGKE*KVDTLSDLYEMLSITQAVIFINTRRKVNWLTQKMHARDFTVT--HGDMDQKEQDMIMREFHYGSS

Parental  RVLITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDI-ETFYN
          ..LITTDLLARG.DV.QVSLVINYDLPTNRE.YIHRIG.GG.FG.KG.AIN.VT.EDK.TL.DI..TFYN
Retrocopy QALITTDLLARGVDV*QVSLVINYDLPTNREIYIHRIGHGGCFGHKGLAINRVTGEDKQTLQDI<QTFYN

Parental  TSIEEMPLNVADLI
          TSIEEMPLNVADLI
Retrocopy TSIEEMPLNVADLI

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	0.20 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_1326 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1326 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1326 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,