RetrogeneDB ID: retro_cjac_727

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:99629775..99630992(+)
• Located in intron of: ENSCJAG00000020442

Retrocopy information

• Ensembl ID: ENSCJAG00000020470
• 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_727
ATGTCTGCGAGTCAGGATTCCCGATCCAGAGACAATGGCCCTGATGGGATGGAGCCCGAAGGCGTCATCGAGAGTAACCG
GAATGAGATTGTTGACAGCTTTGATGACATGAACCTCTCGGAGTCCCTTCTCCGTGGCATCTACGCCTATGGTTTTGAGA
AGCCTTCTGCCATCCAGCAGCGAGCCATTCTACCTTGTATCAAGGGTTATGACGTGACTGCTCAAGCCCAATCTGGGACT
GGGAAAACGGCCACATTTGCCATATCGATTCTGCAGCAGATTGAGTTAGATCTAAAGGCCACCCAGGCCTTGGTCCTAGC
ACCCACTCGAGAATTGGCTCAGCAGATACAGAAGGTGGTTATGGCACTAGGAGACTACATGGGTGCCTCCTGTCATGCCT
GTATTGGGGGCACCAATGTTCGTGCTGAGGTGCAGAAACTGCAGATGGAAGCTCCCCATATCATCGTGGGAACCCCTGGC
CGTGTGTTCGATATGCTTAACCGGAGGTACCTGTCTCCCAAATACATCAAAATGTTTGTACTGGACGAAGCTGATGAAAT
GTTAAGCCGTGGATTCAAGGACCAGATCTATGACATCTTCCAAAAGCTCAACAGCAACACCCAGGTAGTTTTGCCGTCAG
CTACAATGCCTTCTGACGTGCTTGAGGTGACCAAGAAGTTCATGAGGGACCCCATTCGGATTCTTGTCAAGAAGGAAGAG
TTGACCTTGGAGGGTATCCGCCAATTCTACATCAATGTGGAACGAGAGGAATGGAAGCTGGACACACTGTGTGACTTGTA
TGAAACCTTGACCATCACCCAGGCAGTCATCTTCATCAACACCCAAAGGAAGGTGGACTGGCTCACTGAGAAGATGCATG
CTCGATATTTCACTGTCTTTGCCATGCATGGAGATATGGACCAAAAGGAACGAGATGTGATCATGAGGGAGTTTCATTCT
GGCTCTAGCAGAGTTTTGATTACCACAGACCTGCTGGCCAGAGGCATTGATGTGCAGCAGGTTTCTTTAGTCATCAACTA
TGACCTTCCCACCAACAGGAAAACTATATCCACAGAATCGGTCGAGGTGGACGGTTTGGCCGTAAGGGAGTGGCTATTAA
CATGGTGAGAGAAGAAGACAAGCGGAATCTTCGAGAAATAGAGACCTTCAACAACACCTCCATTGAGGAAATGCCCCTCA
ATGTTGCTGACCTCATC

Alignment

ORF - retro_cjac_727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY
          MSASQDSRSRDNGPDGMEPEGVIESN.NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY
Retrocopy MSASQDSRSRDNGPDGMEPEGVIESNRNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGY

Parental  DVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQAQIQKVVMALGDYMGASCHACIGGT
          DV.AQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQ..QIQKVVMALGDYMGASCHACIGGT
Retrocopy DVTAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQ--QIQKVVMALGDYMGASCHACIGGT

Parental  NVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQ
          NVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQ
Retrocopy NVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQ

Parental  VVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIF
          VVL.SATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIF
Retrocopy VVLPSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLCDLYETLTITQAVIF

Parental  INTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYD
          INT.RKVDWLTEKMHAR.FTV.AMHGDMDQKERDVIMREF.SGSSRVLITTDLLARGIDVQQVSLVINYD
Retrocopy INTQRKVDWLTEKMHARYFTVFAMHGDMDQKERDVIMREFHSGSSRVLITTDLLARGIDVQQVSLVINYD

Parental  LPTNR-ENYIHRIGRGGRFGRKGVAINMVTEEDKRTLRDIETFYNTSIEEMPLNVADLI
          LPTNR.ENYIHRIGRGGRFGRKGVAINMV.EEDKR.LR.IETF.NTSIEEMPLNVADLI
Retrocopy LPTNR<ENYIHRIGRGGRFGRKGVAINMVREEDKRNLREIETFNNTSIEEMPLNVADLI

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	2.09 RPM	121.41 RPM
SRP051959_heart	0.84 RPM	66.55 RPM
SRP051959_kidney	1.44 RPM	99.26 RPM
SRP051959_liver	3.01 RPM	195.66 RPM
SRP051959_lung	1.22 RPM	100.79 RPM
SRP051959_lymph_node	1.64 RPM	96.91 RPM
SRP051959_skeletal_muscle	1.14 RPM	69.60 RPM
SRP051959_spleen	1.51 RPM	103.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_727 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_727 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,