RetrogeneDB ID: retro_cjac_2056

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:48890835..48891112(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSR4
• Ensembl ID: ENSCJAG00000011167
• Aliases: None
• Description: signal sequence receptor, delta [Source:HGNC Symbol;Acc:11326]

Sequence

>retro_cjac_2056
TGGGCTGATGTCAGGGAGAACAGCAGTTTCCAGTCGCCTGGGCCCAGGACAGGGTGTTCCCAGCTGTCGTGAAGCATGGA
GCTTCAGGATGCCCATTTGGGTGCCTCTGAGATGAGGTGCTTTGAGAAGGAATCCTGCAGTCTCCTGAGGAGGTCCAAAG
AAATTTTGAGGATATCTCAGCCATCTGTTCCCTGTTCACTGTGGAAGTCGAACACCAGGGCTCCTGGAGGGGCCCTGGGT
CTCCACAGAAGCGCTGGCAGCCACCATCTACTTAATG

Alignment

ORF - retro_cjac_2056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.53 %
• Parental protein coverage: 53.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YADVSGKQFPVTRGQDVGRYQVSWSLDHKSAHAGTYEVRFFDEESYSLLRKA-QRNNEDISIISPLFTVS
          .ADV.........G...G..Q.S.S.....AH.G..E.R.F..ES.SLLR...QRN.EDIS.I..LFTV.
Retrocopy WADVRENSSFQSPGPRTGCSQLS*SMELQDAHLGASEMRCFEKESCSLLRRS<QRNFEDISAICSLFTVE

Parental  VDHRGTWN-GPWVSTEVLAAAIGLV
          V.H.G.W..GPWVSTE.LAA.I.L.
Retrocopy VEHQGSWR<GPWVSTEALAATIYLM

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	0.11 RPM	31.59 RPM
SRP051959_heart	0.14 RPM	13.75 RPM
SRP051959_kidney	0.04 RPM	42.07 RPM
SRP051959_liver	0.06 RPM	39.79 RPM
SRP051959_lung	0.08 RPM	23.86 RPM
SRP051959_lymph_node	0.02 RPM	33.51 RPM
SRP051959_skeletal_muscle	0.20 RPM	11.75 RPM
SRP051959_spleen	0.08 RPM	41.22 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2056 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2056 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2536
Gorilla gorilla	retro_ggor_1585

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011328	1 retrocopy	retro_acar_97,
Callithrix jacchus	ENSCJAG00000011167	1 retrocopy	retro_cjac_2056 ,
Dasypus novemcinctus	ENSDNOG00000025714	2 retrocopies	retro_dnov_1204, retro_dnov_922,
Homo sapiens	ENSG00000180879	1 retrocopy	retro_hsap_2536,
Gorilla gorilla	ENSGGOG00000024329	1 retrocopy	retro_ggor_1585,
Loxodonta africana	ENSLAFG00000006908	1 retrocopy	retro_lafr_337,
Mustela putorius furo	ENSMPUG00000008803	1 retrocopy	retro_mputfur_148,
Nomascus leucogenys	ENSNLEG00000013602	1 retrocopy	retro_nleu_2738,
Otolemur garnettii	ENSOGAG00000006738	1 retrocopy	retro_ogar_691,
Procavia capensis	ENSPCAG00000009037	1 retrocopy	retro_pcap_139,
Sus scrofa	ENSSSCG00000012784	1 retrocopy	retro_sscr_866,