RetrogeneDB ID: retro_cjac_2371

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:117275317..117275683(+)
• Located in intron of: None

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_2371
CATGATCCTACAATAGACAATACTACAGAAAATCAAGTAGAAATACATGCACAACTCTATATGCTTGAAATCTTGAATAC
TACAGGAACAGAACAATTTATAGCAATGAGGGATTTGTACATAAAAAACGAACAAGGCTTTGCATTAGCTTATACCATCC
AACCACAGTCTACATTTTATGATTTACAAGATCTGAGAGAGCAGAGTCTTCAAGTCAAAGACACTGATGACGTCACAATG
ATTCTTGGTAATAAAGGTGACTTGGAAGATAAAAGAGTTGTAGGGAAGGAACAAGGTCAAAATCTAGCAAGACAATGGAA
CAACTGTGCAATCTTAGAATCTTTTCCAAAATAAAAAATAAATGTA

Alignment

ORF - retro_cjac_2371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.8 %
• Parental protein coverage: 66.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQIL
          .DPTI......QVE..AQ..MLEIL.T.GTEQF.AMRDLY.KN.QGFAL.Y.I..QSTF.DLQDLREQ.L
Retrocopy HDPTIDNTTENQVEIHAQLYMLEILNTTGTEQFIAMRDLYIKNEQGFALAYTIQPQSTFYDLQDLREQSL

Parental  RVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINV
          .VKDTDDV.MIL.GNK.DLED.RVVGKEQGQNLARQWNNCA.LES..K.KINV
Retrocopy QVKDTDDVTMIL-GNKGDLEDKRVVGKEQGQNLARQWNNCAILESFPK*KINV

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	0.00 RPM	39.41 RPM
SRP051959_kidney	0.00 RPM	59.21 RPM
SRP051959_liver	0.00 RPM	48.00 RPM
SRP051959_lung	0.00 RPM	114.80 RPM
SRP051959_lymph_node	0.00 RPM	109.97 RPM
SRP051959_skeletal_muscle	0.00 RPM	25.48 RPM
SRP051959_spleen	0.00 RPM	116.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2371 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2371 has 0 orthologous retrocopies within eutheria group .

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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,