RetrogeneDB ID: retro_cjac_605

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:119395855..119396915(-)
• Located in intron of: ENSCJAG00000012600

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAMM50
• Ensembl ID: ENSCJAG00000015070
• Aliases: None
• Description: None

Sequence

>retro_cjac_605
ATGGGGACATTGTACACACAGAGTTTGGAGCCTCTTCCATCAAGTGGATCTGGTTTTGGAGCATCAGAAGATGAAACTGA
ATTTGCTAAAGTTGAAAGTGAAGCTAACAAGAAATTCTTAAAAAAAGATTTGGCTGTTCAACATGCTCATTTTGAAGAGC
TTAGATGGACTAAATAAAGATAATATAATCATTTGGAAAACTGGAGATCCTTTTATGGCTAAAAACCTCACTGAGGTAAT
GTGGAAATCTCATGAAGCTCATGAGAAAGTTATTCATTGAGGAATTTTTAGACAAGTGGATTTTTTGATTGATACATGTC
AAGGTGACAGTGCATTTCCAAATGAGTTAGATGCTACCTTTGAAGTAACTGAATTAAGATTAATGGGCAGTTAAAATACC
ATGGTTGGAAACAATGAAGGGAGTATGGTACGTGGCTTCAAACTCCCTAATCTTCTAGGTCATGCAGAAAAAGTGGCTTT
TCAGTTTTTCTATGGAACAAAAGAAACTTCCTATGGCCTGTCCTTCTTCAAACCAGGGCCCGGAAACTTAAAAAGAAATT
TATCTGTACACTTATATAAGTTACTGAACAGTTCACTTGCAACTCACTTTGGGAGATGAACAGAAGAGTATCAGCCCAGT
AGTTTTTCCATATGGAAAACTAGCCATACCATCAGTTGGAAAGGTGTGTGGCGAGACCTGGGCTGCCACTCAAGGACAGC
ATCATTTGCTGTTTGAAAGGGAAGTCGACATTCACTTAAATCATCTCCTTCACATGCCATGGTCATTGATTTTCAGAATT
CTTCCATCTTACCAAGAAAAGGTACTTTGCTGAAAGTTAACCAGGAACTGACAGGCTACACTGCAAGGGATGTAAGCTTC
ATCAAAGAAGATTTTGAACTTCAGTTGAATAAACCATTCATATCAGATTCAGTTTTTTCAGCACATCTCTGAGGTGGGAT
GTCGGCACCCATGGTGATAAGCCATGAGTCCAGCTGATAGTTTTACCCTGGGGAACGGACAAATGTCCATAGATTCAGCA
TGCACAGCACTGGAGCAGAG

Alignment

ORF - retro_cjac_605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.13 %
• Parental protein coverage: 75.91 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MGTVHARSLEPLPSSGPDFGGLGEEAEFVEVEPEAKQEILENKDVVVQHVHFDGLGRTK-DDIIIC-EIG
          MGT....SLEPLPSSG..FG....E.EF..VE.EA....L..KD..VQH.HF..L..TK..D.II....G
Retrocopy MGTLYTQSLEPLPSSGSGFGASEDETEFAKVESEANKKFLK-KDLAVQHAHFEELRWTK>KDNIIIWKTG

Parental  DVFKAKNLIEVMRKSHEAREKLLRLGIFRQVDVLIDTCQGDDALPNGLDVTFEVTELRRLTGSYNTMVGN
          D.F.AKNL.EVM.KSHEA.EK....GIFRQVD.LIDTCQGD.A.PN.LD.TFEVTEL.RL.GS.NTMVGN
Retrocopy DPFMAKNLTEVMWKSHEAHEKVIH*GIFRQVDFLIDTCQGDSAFPNELDATFEVTEL-RLMGS*NTMVGN

Parental  NEGSMVLGLKLPNLLGRAEKVTFQFSYGTKETSYGLSFFKPRPGSFERNFSVNLYK-VTGQFPWSSLRET
          NEGSMV.G.KLPNLLG.AEKV.FQF.YGTKETSYGLSFFKP.PG...RN.SV.LYK.VT.QF...SL.E.
Retrocopy NEGSMVRGFKLPNLLGHAEKVAFQFFYGTKETSYGLSFFKPGPGNLKRNLSVHLYK<VTEQFTCNSLWEM

Parental  DRGMSAE-YSFP-IWKTSHTVKWEGVWRELGCLSRTASFAVRKESGHSLKSSLSHAMVIDSRNSSILPRR
          .R..SA....FP.IWKTSHT..W.GVWR.LGC.SRTASFAV.K.S.HSLKSS.SHAMVID..NSSILPR.
Retrocopy NRRVSAQ<VVFP<IWKTSHTISWKGVWRDLGCHSRTASFAV*KGSRHSLKSSPSHAMVIDFQNSSILPRK

Parental  GALLKVNQELAGYTGGDVSFIKEDFELQVNKPLIFDSVFSASLWGGMLVPI-GDKP-SSIADRF-YLGGP
          G.LLKVNQEL.GYT..DVSFIKEDFELQ.NKP.I.DSVFSA.L.GGM..P..GDKP..S.AD.F.Y.G..
Retrocopy GTLLKVNQELTGYTARDVSFIKEDFELQLNKPFISDSVFSAHL*GGMSAPM<GDKP<MSPADSF<YPGER

Parental  TSVRGFSMHSIGPQ
          T.V..FSMHS.G..
Retrocopy TNVHRFSMHSTGAE

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	0.47 RPM	10.56 RPM
SRP051959_heart	0.54 RPM	17.75 RPM
SRP051959_kidney	0.95 RPM	17.24 RPM
SRP051959_liver	0.52 RPM	26.47 RPM
SRP051959_lung	1.37 RPM	10.67 RPM
SRP051959_lymph_node	0.30 RPM	13.31 RPM
SRP051959_skeletal_muscle	0.37 RPM	27.06 RPM
SRP051959_spleen	0.95 RPM	17.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_605 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_605 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_605 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4233
Pan troglodytes	retro_ptro_2876
Pongo abelii	retro_pabe_3404
Macaca mulatta	retro_mmul_1152

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015070	2 retrocopies	retro_cjac_2277, retro_cjac_605 ,
Homo sapiens	ENSG00000100347	1 retrocopy	retro_hsap_4233,
Macaca mulatta	ENSMMUG00000015446	1 retrocopy	retro_mmul_1152,
Nomascus leucogenys	ENSNLEG00000015693	1 retrocopy	retro_nleu_1035,
Pongo abelii	ENSPPYG00000011918	1 retrocopy	retro_pabe_3404,
Pan troglodytes	ENSPTRG00000014483	1 retrocopy	retro_ptro_2876,