RetrogeneDB ID: retro_cjac_1876

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:191773024..191774237(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000009322
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1876
TCCGCGGATTATTACAGCAGAGAACATGGTGGCCCAGAGGGAATGTACCCTGATGGTGTCATTGAGAGCAACTGGAATGA
GATTGTTGATAACTTTGATGATATGAATTTAAAGGAGTCTCTTCTTCGGGGCATCTATGCTTACGGTTTTGAGAAGCCTT
CCGCTATTCAGCAGAGAGCTATTATTCCCTGTATTAAAGGGTATGATGTGACTGCTCAAGCTCAGTCAGGTACTGGCAAG
ACAGCCACATTTGCTATTTCCATCCTGCAACAGTTGGAGATTGAGTTCAAGCAGACCCAAGCACTAGTATTGGCCCCCAC
CAGAGAACTGGCTCAACAGATCCAAAAGGTAATTCTGGCACTTGGAGACTATATGGGAGCAACTTGCCATGCCTGCATTG
GTGGAACAAATGTTCGAAATGAAATGCAAAAACTGCAGGCTGAAGCACCACATATTGTGGTTGGTACACCTGGGAGAGTG
TTTGATATGTTAAACAGAAGATACCTTTCTCCCAAATGGATCAAAATGTTTGTTTTGGATGAAGCAGATGAAATGTTGAG
TCGTGGGTTTAAGGATCAAATCTATGAGATTTTCCAAAAACTAAATACAAGTATTCAGGTTGTGTTGCTTTCTGCCACAA
TGCCAACTGATGTGTTGGAAGTGACCAAAAAATTCATGAGAGATCCAATTCGAATTCTGGTGAAAAAGGAAGAACTGACC
CTTGAAGGAATCAAACAGTTTTATATTAATGTTGAGAGAGAGGAATGGAAGTTGGATACACTTTGTGACTTGTATGAGAC
ACTGACCATTACACAGGCTGTTATTTTTTCTCAATACAAGGCGCAAGGTGGACTGGCTGACTGAGAAAATGCATGCCAGA
GACTTCACAGTTTCTGCTCTGCATGGTGACATAGACCAGAAGGAGAGAGATGTTATCATGAGGGAATTCCGATCAGGGTC
AAGCCGTGTTCTGATAACTACTGACTTGTTGGCTCGTGGGATTGATGTGCAACAAGTGTCTTTGGTTATAAATTATGATC
TCCCTACCAATCGTGAAAACTATATTCACAGAATTGGCAGAGGGGGTCGATTTGGGAGGAAAGGTGTGGCTATAAACTTT
GTTACTGAAGAAGACAAGAGGATTCTTCGTGACATTGAGACTTTCTACAATACTACAGTGGAGGAGATGTCCATGAATGT
GGCTGATCTTATT

Alignment

ORF - retro_cjac_1876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.19 %
• Parental protein coverage: 99.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQDSRSRDNG-PDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDV
          S.D..SR..G.P.GM.P.GVIESNWNEIVD.FDDMNL.ESLLRGIYAYGFEKPSAIQQRAI.PCIKGYDV
Retrocopy SADYYSREHGGPEGMYPDGVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDV

Parental  IAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQAQIQKVVMALGDYMGASCHACIGGTNV
          .AQAQSGTGKTATFAISILQQ.E...K.TQALVLAPTRELAQQ..IQKV..ALGDYMGA.CHACIGGTNV
Retrocopy TAQAQSGTGKTATFAISILQQLEIEFKQTQALVLAPTRELAQQ--IQKVILALGDYMGATCHACIGGTNV

Parental  RAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVV
          R.E.QKLQ.EAPHI.VGTPGRVFDMLNRRYLSPK.IKMFVLDEADEMLSRGFKDQIY.IFQKLN...QVV
Retrocopy RNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVV

Parental  LLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIF-I
          LLSATMP.DVLEVTKKFMRDPIRILVKKEELTLEGI.QFYINVEREEWKLDTLCDLYETLTITQAVIF..
Retrocopy LLSATMPTDVLEVTKKFMRDPIRILVKKEELTLEGIKQFYINVEREEWKLDTLCDLYETLTITQAVIF>L

Parental  NTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL
          NTRRKVDWLTEKMHARDFTVSA.HGD.DQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL
Retrocopy NTRRKVDWLTEKMHARDFTVSALHGDIDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDL

Parental  PTNRENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
          PTNRENYIHRIGRGGRFGRKGVAIN.VTEEDKR.LRDIETFYNT..EEM..NVADLI
Retrocopy PTNRENYIHRIGRGGRFGRKGVAINFVTEEDKRILRDIETFYNTTVEEMSMNVADLI

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	8.08 RPM	121.41 RPM
SRP051959_heart	21.61 RPM	66.55 RPM
SRP051959_kidney	24.36 RPM	99.26 RPM
SRP051959_liver	14.64 RPM	195.66 RPM
SRP051959_lung	14.59 RPM	100.79 RPM
SRP051959_lymph_node	20.50 RPM	96.91 RPM
SRP051959_skeletal_muscle	32.19 RPM	69.60 RPM
SRP051959_spleen	20.50 RPM	103.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1876 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1876 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,