RetrogeneDB ID: retro_cjac_2679

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:150148558..150149402(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4A1
• Ensembl ID: ENSCJAG00000015114
• Aliases: None
• Description: eukaryotic initiation factor 4A-I [Source:RefSeq peptide;Acc:NP_001192066]

Sequence

>retro_cjac_2679
GTGGTCATGGCACTAGGATACTACCTGGGTACCTCCTGTCATGCCTGTATTGGGGGCACCATGTGTGCTGAGGCGCAGAG
ACTGCAGATGGAAGCTCCCCATATCATCATGGGTACCCCTGACTGTGTGTTTGGTATGCTTAACTGGAGATACCTGTCTC
CCAAATACATCAAGAGGTTTGTACTGAACACAGCTGATGAAATGTTAAGCCATGGATTCAAAGACCAGATCTATGAAATA
TTCCAAAAGCTCAACAGCAACACCCAGGTATTTTTGCTGTCAGCTACAATGCCTTCTGATATGCTTGAGGTGACCAAGAA
GTTCATGAGGGACCCCATTCGGATTCTTTCCAAGATGGAAGAGTTGACCCTGGAGGGTATCTGCCAATTCTACATGAACG
TGAAAGGAGAGGAGTAAAAGCTGGACATGCTGTGTGACTTGTATGAAACCCTGACCATCACCCAGGCAGTCATCTTCATC
AACATCCAAAGGAAGGTGGACTGGCTCACCAAGAAGATGCATGCTTGTGATTTCACTGTCTCTGCCATGCATGGAGATAC
GGACCAAAAAAACGAGATGTGATCATGAGGGAGTTTGGTTCTGGCTCTAGCACAGTTTGGTTACCACTGACCTGCTGGCC
AGAGGCATTGATGAGGTTTCTTTAGTCATCAACTATTTCCTTCCCACCAACAGGAAAAACTATATCCACGGAATCAGTCG
AGGGGGATAGTTTGGCTGTAAGGGTATGGCTATTTACATCTTAATAGAAGACAAGAGGACTCTTTGAGACACCTTCTACA
ACACTGCCATTGAGGAAATGCCCCTCAATGTTGCTGACCTCATC

Alignment

ORF - retro_cjac_2679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 70.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEML
          VVMALG.Y.G.SCHACIGGT...AE.Q.LQMEAPHII.GTP..VF.MLN.RYLSPKYIK.FVL..ADEML
Retrocopy VVMALGYYLGTSCHACIGGT-MCAEAQRLQMEAPHIIMGTPDCVFGMLNWRYLSPKYIKRFVLNTADEML

Parental  SRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEW
          S.GFKDQIY.IFQKLNSNTQV.LLSATMPSD.LEVTKKFMRDPIRIL.K.EELTLEGI.QFY.NV..EE.
Retrocopy SHGFKDQIYEIFQKLNSNTQVFLLSATMPSDMLEVTKKFMRDPIRILSKMEELTLEGICQFYMNVKGEE*

Parental  KLDTLCDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQ-KERDVIMREFRSGSSRV-L
          KLD.LCDLYETLTITQAVIFIN..RKVDWLT.KMHA.DFTVSAMHGD.DQ.K.RDVIMREF.SGSS.V.L
Retrocopy KLDMLCDLYETLTITQAVIFINIQRKVDWLTKKMHACDFTVSAMHGDTDQ<KKRDVIMREFGSGSSTV<L

Parental  ITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIE
          .TTDLLARGID...VSLVINY.LPTNR.NYIH.I.RGG.FG.KG.AI.....EDKRTL.D..TFYNT.IE
Retrocopy VTTDLLARGID--EVSLVINYFLPTNRKNYIHGISRGG*FGCKGMAIYILI-EDKRTL*D--TFYNTAIE

Parental  EMPLNVADLI
          EMPLNVADLI
Retrocopy EMPLNVADLI

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
SRP051959_colon	0.11 RPM	121.41 RPM
SRP051959_heart	0.12 RPM	66.55 RPM
SRP051959_kidney	0.13 RPM	99.26 RPM
SRP051959_liver	0.04 RPM	195.66 RPM
SRP051959_lung	0.18 RPM	100.79 RPM
SRP051959_lymph_node	0.02 RPM	96.91 RPM
SRP051959_skeletal_muscle	0.04 RPM	69.60 RPM
SRP051959_spleen	0.08 RPM	103.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2679 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2679 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2679 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016753	1 retrocopy	retro_amel_1300,
Callithrix jacchus	ENSCJAG00000015114	8 retrocopies	retro_cjac_1876, retro_cjac_2046, retro_cjac_2521, retro_cjac_2679 , retro_cjac_3086, retro_cjac_3203, retro_cjac_395, retro_cjac_727,
Dipodomys ordii	ENSDORG00000014225	1 retrocopy	retro_dord_732,
Macropus eugenii	ENSMEUG00000010780	2 retrocopies	retro_meug_158, retro_meug_179,
Microcebus murinus	ENSMICG00000014759	2 retrocopies	retro_mmur_1164, retro_mmur_1477,
Myotis lucifugus	ENSMLUG00000003415	3 retrocopies	retro_mluc_1047, retro_mluc_1229, retro_mluc_1805,
Macaca mulatta	ENSMMUG00000013499	1 retrocopy	retro_mmul_1280,
Monodelphis domestica	ENSMODG00000007090	3 retrocopies	retro_mdom_1282, retro_mdom_326, retro_mdom_711,
Otolemur garnettii	ENSOGAG00000008132	2 retrocopies	retro_ogar_1375, retro_ogar_1862,
Ochotona princeps	ENSOPRG00000008591	2 retrocopies	retro_opri_155, retro_opri_985,
Sorex araneus	ENSSARG00000006017	7 retrocopies	retro_sara_224, retro_sara_383, retro_sara_461, retro_sara_567, retro_sara_6, retro_sara_605, retro_sara_89,