RetrogeneDB ID: retro_cjac_607

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:120647264..120647669(-)
• Located in intron of: ENSCJAG00000012733

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1B
• Ensembl ID: ENSCJAG00000007261
• Aliases: None
• Description: RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]

Sequence

>retro_cjac_607
CAGTGTATGCTAGAAATCTGGGATACTGCAGGAATGGAATGATTTACAGCAATGAGGGATTTGTACATGAAAAATGGACA
AGGCTCTGCATTAGTTTATTCCATCACAGCACAGTTCACATGTAACAATTTACAAGACCTGAGAGAATAGAGTCTTTCAG
TTAAAGACACTGATGATGTTCCAATGATTCTTGTTGGTAATAATTGTGACTTGGAAGATGAAAGAGTTGTAGGGAAGAAA
CAAGGTCAAAATCTAGCCAGACAATGGAACAACTGTGCATTCTTAGAATCTTCTGCAAAATCAAAAATAAGTTTTAATGA
GATCTTTTATGACCTAGTGCAGCAAATTAACAGAAAAACTCCAGTGCCTGGGAAGGCTCGCAAAAAGTTGTCATGTCAGC
TGCTT

Alignment

ORF - retro_cjac_607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.15 %
• Parental protein coverage: 73.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCD
          QCMLEI.DTAG.E.FTAMRDLYMKNGQG.ALVYSITAQ.T.N.LQDLRE..L.VKDTDDVPMILVGN.CD
Retrocopy QCMLEIWDTAGME*FTAMRDLYMKNGQGSALVYSITAQFTCNNLQDLRE*SLSVKDTDDVPMILVGNNCD

Parental  LEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
          LEDERVVGK.QGQNLARQWNNCAFLESSAKSKI..NEIFYDLV.QINRKTPVPGKARKK.SCQLL
Retrocopy LEDERVVGKKQGQNLARQWNNCAFLESSAKSKISFNEIFYDLVQQINRKTPVPGKARKKLSCQLL

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	81.38 RPM
SRP051959_heart	0.16 RPM	39.41 RPM
SRP051959_kidney	0.07 RPM	59.21 RPM
SRP051959_liver	0.00 RPM	48.00 RPM
SRP051959_lung	0.05 RPM	114.80 RPM
SRP051959_lymph_node	0.07 RPM	109.97 RPM
SRP051959_skeletal_muscle	0.00 RPM	25.48 RPM
SRP051959_spleen	0.11 RPM	116.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_607 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_607 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_607 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4234
Pan troglodytes	retro_ptro_2877
Gorilla gorilla	retro_ggor_2836
Pongo abelii	retro_pabe_3403
Macaca mulatta	retro_mmul_1151

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008637	1 retrocopy	retro_amel_103,
Callithrix jacchus	ENSCJAG00000007261	3 retrocopies	retro_cjac_1435, retro_cjac_2371, retro_cjac_607 ,
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
Callithrix jacchus	ENSCJAG00000036517	1 retrocopy	retro_cjac_2400,
Cavia porcellus	ENSCPOG00000008272	4 retrocopies	retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Gorilla gorilla	ENSGGOG00000025649	1 retrocopy	retro_ggor_2836,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Mus musculus	ENSMUSG00000052681	1 retrocopy	retro_mmus_1370,
Nomascus leucogenys	ENSNLEG00000003573	2 retrocopies	retro_nleu_1034, retro_nleu_481,
Otolemur garnettii	ENSOGAG00000005746	2 retrocopies	retro_ogar_2260, retro_ogar_272,
Sarcophilus harrisii	ENSSHAG00000011497	1 retrocopy	retro_shar_425,
Sus scrofa	ENSSSCG00000030014	2 retrocopies	retro_sscr_435, retro_sscr_909,
Tupaia belangeri	ENSTBEG00000013380	4 retrocopies	retro_tbel_2145, retro_tbel_4650, retro_tbel_4658, retro_tbel_613,