RetrogeneDB ID: retro_cjac_553

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:77029222..77029571(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004797
• Aliases: None
• Description: None

Sequence

>retro_cjac_553
GACCAAACCACCCTGGTAGAACAAACAAAAAGAATAAAATAAATGGAAGCTGTTGAAAGTGATTCCTTTGTTCAGCAGAC
ATTCAGATCAATTAAGAAGTCAAAAAGTTAGTGGAATCTACTGAAGCACAACATGCAACTTCAACATCAGGACCAGCATC
ACTAGGTGTTGATCCACTCAGTACCAAAAATGAAATAGAAATGAGCAGCATTCCTACCGCCATCAGGTACCAAGATGACA
ATTCCCTGGCCCATCCGCATTTATTTAGAGAGAAAGCTGATGCTGAGGGAAAATGATTCAGAGGCTAATTGCATTCTGAC
AAGAAAGACTAATGGGCAGTCCTGTGGCC

Alignment

ORF - retro_cjac_553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DQATLVEQVKRVKEIEAIESDSFVQQTFRSSK-EVKKSVEPSEVKQTTSTSGPASAVVEPPSTEKEIDPS
          DQ.TLVEQ.KR.K..EA.ESDSFVQQTFRS.K.EVKK.VE..E....TSTSGPAS..V.P.ST..EI..S
Retrocopy DQTTLVEQTKRIK*MEAVESDSFVQQTFRSIK<EVKKLVESTEAQHATSTSGPASLGVDPLSTKNEIEMS

Parental  SIPTAIKYQDDNSLAHPNLFIEKADAEERWFK-RLIALRQERLMGSPVA
          SIPTAI.YQDDNSLAHP.LF.EKADAE...F..RLIA..QERLMGSPVA
Retrocopy SIPTAIRYQDDNSLAHPHLFREKADAEGK*FR<RLIAF*QERLMGSPVA

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	1.75 RPM
SRP051959_heart	0.00 RPM	1.44 RPM
SRP051959_kidney	0.02 RPM	1.86 RPM
SRP051959_liver	0.02 RPM	2.38 RPM
SRP051959_lung	0.00 RPM	1.81 RPM
SRP051959_lymph_node	0.00 RPM	2.08 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.03 RPM
SRP051959_spleen	0.00 RPM	2.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_553 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_553 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_553 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004797	1 retrocopy	retro_cjac_553 ,
Cavia porcellus	ENSCPOG00000000876	2 retrocopies	retro_cpor_618, retro_cpor_671,
Echinops telfairi	ENSETEG00000017217	1 retrocopy	retro_etel_1555,
Homo sapiens	ENSG00000174891	1 retrocopy	retro_hsap_4281,
Mus musculus	ENSMUSG00000034544	1 retrocopy	retro_mmus_666,
Nomascus leucogenys	ENSNLEG00000004137	1 retrocopy	retro_nleu_2851,
Rattus norvegicus	ENSRNOG00000012639	2 retrocopies	retro_rnor_2454, retro_rnor_577,
Tupaia belangeri	ENSTBEG00000001973	13 retrocopies	retro_tbel_1285, retro_tbel_1372, retro_tbel_2078, retro_tbel_2400, retro_tbel_2545, retro_tbel_3145, retro_tbel_3313, retro_tbel_3748, retro_tbel_3834, retro_tbel_4317, retro_tbel_4458, retro_tbel_4494, retro_tbel_840,