RetrogeneDB ID: retro_cjac_3014

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:113841306..113841910(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIT2
• Ensembl ID: ENSCJAG00000000590
• Aliases: None
• Description: nitrilase family, member 2 [Source:HGNC Symbol;Acc:29878]

Sequence

>retro_cjac_3014
GCAACTTTCCACTTGGCCGTCACCCAGCTTCAAGTTTCTTTATCAAATCAGATTACAACACTCAAGCTTGTAGCCTTGTC
CGGGAGACAGCAGTGCAAGGAGCCAAAATAGTTTCTTTGCTGGAATGCTTTAATTCTCCATATGGCACAAAATATTTTCT
CGAATATGCAGCGAAAATTCCTGGTAAATCCACACAGAAGCTTTCTGAAGTAGCAAAGGAATACAGCCTCACTAGAGGCT
TCATCCCAGAAGAGGATGCCGGGAAATTATATAACACCTGTGCTGTGTTTGCACCTTATGGAACTTTACTAGTAAAGCAC
AGAACGGTCCATCTGCTTGACACTGGTGTTCCTGGAAAAATGACATTTCAAGAATCTTAAAAACGTTGAGTCTGGGCAAT
AGTTTTTCCATATTTGATACTCCCTACCGCAGAATGGGTCTAGCCATCAGCTACGACGTCCGGTTTGCAGAGCTTGCACA
GATCTATACACAGAGAGGCTGCCAGCTATTGGTATATTCAGGGGCTTTCAGTTGGAGCACTGAACCAGCCCACTGAGAAT
TGCTTCAGGCTCTTGATAATCAGGTGTATGTGGCCACACTCTCC

Alignment

ORF - retro_cjac_3014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.19 %
• Parental protein coverage: 74.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SAFRLALIQLHISS-IKSENVTRACSLIREAATQGAKIVSLPECFNSPYGVKYFPEYAEKIPGESTQKLS
          ..F.LA..QL..S..IKS...T.ACSL.RE.A.QGAKIVSL.ECFNSPYG.KYF.EYA.KIPG.STQKLS
Retrocopy ATFHLAVTQLQVSL<IKSDYNTQACSLVRETAVQGAKIVSLLECFNSPYGTKYFLEYAAKIPGKSTQKLS

Parental  EVAKECSIYLIGVKGSIPEEDAGKLYNTCTVFGPDGTLLAKYRKIHLFDIDVPGKITFQES-KTLSPG-D
          EVAKE.S.......G.IPEEDAGKLYNTC.VF.P.GTLL.K.R..HL.D..VPGK.TFQES.K....G..
Retrocopy EVAKEYSL----TRGFIPEEDAGKLYNTCAVFAPYGTLLVKHRTVHLLDTGVPGKMTFQES>KNVESG>N

Parental  SFSTFDTPYCRVGLGICYDMRFAELAQIYTQRGCQLLVYPGAFNLTTGPAHWELLQRGRAVDNQVYVATV
          SFS.FDTPY.R.GL.I.YD.RFAELAQIYTQRGCQLLVY.GAF...T.PAH.ELLQ...A.DNQVYVAT.
Retrocopy SFSIFDTPYRRMGLAISYDVRFAELAQIYTQRGCQLLVYSGAFSWSTEPAH*ELLQ---ALDNQVYVATL

Parental  S
          S
Retrocopy S

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	7.19 RPM
SRP051959_heart	0.00 RPM	16.05 RPM
SRP051959_kidney	0.00 RPM	92.47 RPM
SRP051959_liver	0.00 RPM	143.59 RPM
SRP051959_lung	0.00 RPM	13.58 RPM
SRP051959_lymph_node	0.00 RPM	13.38 RPM
SRP051959_skeletal_muscle	0.00 RPM	16.92 RPM
SRP051959_spleen	0.00 RPM	23.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3014 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3014 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3014 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_411
Pan troglodytes	retro_ptro_315
Gorilla gorilla	retro_ggor_406
Macaca mulatta	retro_mmul_505

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003980	1 retrocopy	retro_amel_1002,
Callithrix jacchus	ENSCJAG00000000590	1 retrocopy	retro_cjac_3014 ,
Homo sapiens	ENSG00000114021	1 retrocopy	retro_hsap_411,
Gorilla gorilla	ENSGGOG00000003724	1 retrocopy	retro_ggor_406,
Macaca mulatta	ENSMMUG00000020024	2 retrocopies	retro_mmul_1758, retro_mmul_505,
Mustela putorius furo	ENSMPUG00000011450	1 retrocopy	retro_mputfur_805,
Nomascus leucogenys	ENSNLEG00000002631	1 retrocopy	retro_nleu_1009,
Pan troglodytes	ENSPTRG00000015161	1 retrocopy	retro_ptro_315,