RetrogeneDB ID: retro_cjac_2357

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:99433545..99434298(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARG2
• Ensembl ID: ENSCJAG00000015277
• Aliases: None
• Description: None

Sequence

>retro_cjac_2357
CTAAGGAACAGCCTGTCAAGCCTCCTCTGGATGCAAGTGCATTGTGTCCTGGTTGTGATAGGAGCCCTGTTCTTGTAGGG
ACAGAAAAAGAAAAGGAGTGAAACATGGTCCAGCTGCCAGAAGAAAAGTTGGATTGGTAAAAAGGGTCTCCAACTTGGGC
TGCTGCCTAAATGACTTTGGAAATTTTAGTCTACTCCAATCCCCGCAGATGAGCTGTTTAACAACCCAGCAGTGAATCTG
TGCTCAGTGCCCCAGCCAACCAGCAACTGGCTGAGCTGGTTAGTAGAGCAGTTGTTTTATGGCTACAGCTACATCACAGT
GAGAGGATACCACAGCCTGGCTATTAGTACCATTAGTGGCCATGCCTGGAACTGCCACAACCTTTGTGTCACTTGGGTTG
ATGCCCATGCAGACATCAGTACACCTCTTACCACTTCATCAGGAAATATCCGTGGACTATTAGTTTCAATTCCCCTCAGA
GAACTACAAGGAAAGATACCATAATTTCTGTGATTTTCCTGGATAAACCTTGTATCTCTTCCCCAAGTACTGTTTTCTGG
TAGAGGAGATGTGGACCCTCTGGAACATTTTTTTTTTTTAAAGAACAATGATATCTAGTATTTTTCCATGAGAGACACTG
ATCCACTTGGTACCCAGAAGGTTACGGAACAGAAATTTGATCTGCTGACTGGAAAATGACAAAGGTCTGTCCATCTGAGT
TTTGATACTGAAGTATTTGACTCTATGCTGGCT

Alignment

ORF - retro_cjac_2357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.7 %
• Parental protein coverage: 70.62 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LQTRVHSILKKSVHSV-AVIGAPFSQGQK-RKGVEHGPAAIREAGLMKRLSSLGCHLKDFGDLSF-TPVP
          L.....S.L...VH.V..VIGA.F..GQK.RKGV.HGPAA.R..GL.KR.S.LGC.L.DFG..S..TP.P
Retrocopy LRNSLSSLLWMQVHCVLVVIGALFL*GQK>RKGVKHGPAARRKVGLVKRVSNLGCCLNDFGNFSL<TPIP

Parental  KDDLYNNLIVNPRSV-GLANQELAEVVSRAVS-DGYSCVTLGGDHSLAIGTISGHARHCPDLCVIWVDAH
          .D.L.NN..VN..SV...ANQ.LAE.VSRAV...GYS..T..G.HSLAI.TISGHA..C..LCV.WVDAH
Retrocopy ADELFNNPAVNLCSV<APANQQLAELVSRAVV>YGYSYITVRGYHSLAISTISGHAWNCHNLCVTWVDAH

Parental  ADINTPLTTSSGNLHGQPVSFLLRELQDKVPQLPGFSWI-KPCISSPSIVYIGLRDVDPPEHFILK-NYD
          ADI.TPLTTSSGN..G..VS..LRELQ.K.P....FSWI.KPCISSPS.V....R.......F..K.N.D
Retrocopy ADISTPLTTSSGNIRGLLVSIPLRELQGKIP*FL*FSWI<KPCISSPSTVFW*RRCGPSGTFFFFK>NND

Parental  IQYFSMRDIDRLGIQKVMEQTFDLLIGKRQRPIHLSFDIDAFDPTLA
          I.YFSMRD.D.LG.QKV.EQ.FDLL.GK.QR..HLSFD...FD..LA
Retrocopy I*YFSMRDTDPLGTQKVTEQKFDLLTGK*QRSVHLSFDTEVFDSMLA

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	4.64 RPM
SRP051959_heart	0.00 RPM	4.91 RPM
SRP051959_kidney	0.00 RPM	50.56 RPM
SRP051959_liver	0.00 RPM	17.61 RPM
SRP051959_lung	0.00 RPM	4.83 RPM
SRP051959_lymph_node	0.00 RPM	4.75 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.46 RPM
SRP051959_spleen	0.00 RPM	5.23 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2357 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2357 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2357 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3501
Pan troglodytes	retro_ptro_2373
Gorilla gorilla	retro_ggor_2367
Pongo abelii	retro_pabe_2893

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005722	1 retrocopy	retro_acar_91,
Choloepus hoffmanni	ENSCHOG00000007159	1 retrocopy	retro_chof_1179,
Callithrix jacchus	ENSCJAG00000015277	4 retrocopies	retro_cjac_1933, retro_cjac_2357 , retro_cjac_2561, retro_cjac_902,
Dasypus novemcinctus	ENSDNOG00000004808	1 retrocopy	retro_dnov_251,
Homo sapiens	ENSG00000081181	1 retrocopy	retro_hsap_3501,
Gorilla gorilla	ENSGGOG00000005615	1 retrocopy	retro_ggor_2367,
Monodelphis domestica	ENSMODG00000009978	1 retrocopy	retro_mdom_257,
Nomascus leucogenys	ENSNLEG00000000741	2 retrocopies	retro_nleu_2875, retro_nleu_792,
Oryctolagus cuniculus	ENSOCUG00000000584	1 retrocopy	retro_ocun_277,
Pongo abelii	ENSPPYG00000005926	1 retrocopy	retro_pabe_2893,
Pan troglodytes	ENSPTRG00000006467	1 retrocopy	retro_ptro_2373,