RetrogeneDB ID: retro_cjac_968

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:32774235..32775408(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2A
• Ensembl ID: ENSCJAG00000001199
• Aliases: None
• Description: None

Sequence

>retro_cjac_968
TATGTTCCAGGGAGTAGGGATGCAACTTCATTTGTTGCATTATATTTGTACCCCGACTTTGTTAGACCTCATGCAGCTTT
AGCCAACAGCAATTTCTCTAAGCCAATGACATTACAATGCTGTGGAATGAAAAAGCCACTGCTGGCTTGTAATAGTAAGA
ACAGATGTTGACAAGAGAACTTCCTGCTATGGGGAACAAAGGCTGAATTACACTGCAACAAATGGAGAAAGTTCTGTCAT
TTGTTCAATTACCAAAACGTAGCCCCATTTATGATATAATTTGGAAATCTGGTTCTACTGAGTTTTATGCTATTTATAGT
TTTATGCTTGCCAAAGCTATGATTTTCAACTTGAAATGTGATCTTGTGTTTGACCTTGGAACTGGTGCTCTAAGGCAGCC
TATTTGGCCTTTGTGGCCAGGTATTAATACTAACTGGATTTGGAAATCTGAGGGACAGACACGAGTGTGGGATATTAAAA
GCTACAAACTTATTTCCAAACAAGTAGCCTCTGATCCTGCATATTTTGCTAGGTACCTATAAGGGAGCACATTTTACTAC
CACACATGCTCCCAGGTTGTGTGTTAATAATGGACACAAGCTTTGGCATTATATCAGCCCTATCCTGAATGAGTAAGATA
TGTCATCAAATGCAGAAATAAGGCAGGTTTCTTGGCAGCCATTTCTGGATGGACTATTTCCAGCAAAAGCGGTAACTTTT
CAAGCAGTTCCAAGTCAAGTACCCAACTAGGAACCTAAATTTGCAGTTACTGATAGACTCCCAGCTTTAAGAAATAAACC
AATCAACAATTCCAAGCTGCATCAAGAGAAATCACCCCAGAATAAGAAATCACAACCAGGAAATGATAAACCATTATCAA
AAGCAGCCCTTAACAAATCAAAGGAAATATGAAGCTGAGAAAGCTACAAAGCAGGAAGTAAGAAGTGACGAGTCCAGATT
TGACACCTACCCTGTCCCACAGAGCACACCCTGAAATACAGGGTCTCGGTTAATGTCTGGAAACCCTGAGATAGACGAAA
AATTCAAGAACTGAAAAAGACAAAAGCAACTGAACCTTGAAAGAACACAGCAACTGAAACGCAGCCAGAAAAACAATGAG
TTAGAAAAATAAAAGATATTTCTCTTCTCCAAGAGCTGGAAGATTTGAAAATG

Alignment

ORF - retro_cjac_968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.25 %
• Parental protein coverage: 66.39 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  YVPGSKGAPSFVRLYQYPNFAGPHAALANKSFFK-ADKVTMLWNKKATAVL-VIASTEVDKTGASYYGEQ
          YVPGS..A.SFV.LY.YP.F..PHAALAN..F.K.A...TMLWN.KATA.L.VI..T.VDK...S.YGEQ
Retrocopy YVPGSRDATSFVALYLYPDFVRPHAALANSNFSK<ANDITMLWNEKATAGL<VIVRTDVDKR-TSCYGEQ

Parental  TLHYIATNGESAVV-QLPKNGP-IYDVVWNSSSTEFCAVYGFMPAKATIFNLKCDPVFDFGTGP-RNAAY
          .L.Y.ATNGES.V.....K..P.IYD..W.S.STEF.A.Y.FM.AKA.IFNLKCD.VFD.GTG....AAY
Retrocopy RLNYTATNGESSVICSITKT*P>IYDIIWKSGSTEFYAIYSFMLAKAMIFNLKCDLVFDLGTGA<SKAAY

Parental  -YSPHGHILVLAGFGNLR-GQMEVWDVKNYKLISKPVASDSTYFAW-CPDGEHIL-TATCAPRLRVNNGY
          .....G..L.L.GFGNLR.GQ..VWD.K.YKLISK.VASD..YFA...P..EHIL.T.T.APRL.VNNG.
Retrocopy <FGLCGQVLILTGFGNLR<GQTRVWDIKSYKLISKQVASDPAYFAR<VPIREHIL<TTTHAPRLCVNNGH

Parental  KIWHYTGSILHKYDVPSNAELWQVSWQPFLDGIFPAKTITYQAVPSEVPNEEPKVATAYRPPALRNKPIT
          K.WHY...IL...D..SNAE..QVSWQPFLDG.FPAK..T.QAVPS.VPN.EPK.A...R.PALRNKPI.
Retrocopy KLWHYISPILNE*DMSSNAEIRQVSWQPFLDGLFPAKAVTFQAVPSQVPN*EPKFAVTDRLPALRNKPIN

Parental  NSKLHEEEPPQNMKPQSGNDKPLSKTALK-NQRKHEAKKAAKQEARSDKSPDLTPTPAPQSTPRSTISQS
          NSKLH.E..PQN.K.Q.GNDKPLSK.AL..NQRK.EA.KA.KQE.RSD.S......P.PQSTP..T.S..
Retrocopy NSKLHQEKSPQNKKSQPGNDKPLSKAALN>NQRKYEAEKATKQEVRSDES-RFDTYPVPQSTP*NTGSRL

Parental  ISGDPEIDKKIKN-LKKKLKAIEQLKEQAATGKQLEKNQLEKIQKETALLQELEDLEL
          .SG.PEID.K.KN.LK.K.KA.E..K...AT..Q.EK....KI.K...LLQELEDL..
Retrocopy MSGNPEIDEKFKN<LK-KTKATEP*K-NTATETQPEKQ*VRKI-KDISLLQELEDLKM

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	0.00 RPM	28.80 RPM
SRP051959_heart	0.00 RPM	35.68 RPM
SRP051959_kidney	0.00 RPM	34.61 RPM
SRP051959_liver	0.00 RPM	66.43 RPM
SRP051959_lung	0.00 RPM	28.87 RPM
SRP051959_lymph_node	0.00 RPM	33.06 RPM
SRP051959_skeletal_muscle	0.00 RPM	59.62 RPM
SRP051959_spleen	0.00 RPM	34.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_968 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_968 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001199	1 retrocopy	retro_cjac_968 ,
Dasypus novemcinctus	ENSDNOG00000014002	1 retrocopy	retro_dnov_1148,
Homo sapiens	ENSG00000144895	1 retrocopy	retro_hsap_565,
Gorilla gorilla	ENSGGOG00000015391	1 retrocopy	retro_ggor_509,
Loxodonta africana	ENSLAFG00000003767	1 retrocopy	retro_lafr_502,
Macaca mulatta	ENSMMUG00000017696	1 retrocopy	retro_mmul_2395,
Nomascus leucogenys	ENSNLEG00000003219	1 retrocopy	retro_nleu_2213,
Oryctolagus cuniculus	ENSOCUG00000016095	3 retrocopies	retro_ocun_1771, retro_ocun_1825, retro_ocun_1861,
Pongo abelii	ENSPPYG00000029636	2 retrocopies	retro_pabe_517, retro_pabe_652,
Pan troglodytes	ENSPTRG00000015528	1 retrocopy	retro_ptro_423,
Ictidomys tridecemlineatus	ENSSTOG00000003374	1 retrocopy	retro_itri_1706,