RetrogeneDB ID: retro_cjac_1102

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:58763856..58764198(+)
• Located in intron of: ENSCJAG00000020517

Retrocopy information

• Ensembl ID: ENSCJAG00000020524
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003568
• Aliases: None
• Description: SH3 domain-binding glutamic acid-rich-like protein [Source:UniProtKB/TrEMBL;Acc:F7GVV1]

Sequence

>retro_cjac_1102
ATGGTGATCCGTGTATATATCGCATCTTCCTCTGGCTCTACGGCGATTAAGAAGAAACAGCAGGATGTGCTTGGTTTCCT
AGAAGCCAACAAAATAGGATTTGAAGAAAAAGATATTGCAGCCAATGAAGAGAATCGGAAGTGGATGAGAGAAAATGTAC
CTGAAAATAGTCGACCAGCCACAGGGTACCCCCTGCCACCTCAGATTTTCAATGAAAGCCAGTATCGAGGGGACTATGAT
GCTTTCTTTGAAGCCAGAGAAAATAATGCAGTGTATGCCTTCTTAGGCATGACAGCCCCTCCTGGTTCAAAGGAAGCAGA
AGTGCAAGCAAAGCAGCAAGCA

Alignment

ORF - retro_cjac_1102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVIRVYIASSSGSTAIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGYPLPPQIF
          MVIRVYIASSSGSTAIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGYPLPPQIF
Retrocopy MVIRVYIASSSGSTAIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGYPLPPQIF

Parental  NESQYRGDYDAFFEARENNAVYAFLGLTAPPGSKEAEVQAKQQA
          NESQYRGDYDA....................GSKEAEVQAKQQA
Retrocopy NESQYRGDYDAXXXXXXXXXXXXXXXXXXXXGSKEAEVQAKQQA

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	1.33 RPM	4.37 RPM
SRP051959_heart	1.79 RPM	5.95 RPM
SRP051959_kidney	0.80 RPM	3.19 RPM
SRP051959_liver	0.52 RPM	1.58 RPM
SRP051959_lung	1.32 RPM	5.34 RPM
SRP051959_lymph_node	1.16 RPM	3.31 RPM
SRP051959_skeletal_muscle	0.26 RPM	0.63 RPM
SRP051959_spleen	2.33 RPM	6.89 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1102 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1102 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004130	1 retrocopy	retro_chof_647,
Callithrix jacchus	ENSCJAG00000003568	2 retrocopies	retro_cjac_1102 , retro_cjac_140,
Cavia porcellus	ENSCPOG00000012267	3 retrocopies	retro_cpor_1172, retro_cpor_244, retro_cpor_844,
Dipodomys ordii	ENSDORG00000011106	2 retrocopies	retro_dord_199, retro_dord_588,
Equus caballus	ENSECAG00000012612	1 retrocopy	retro_ecab_648,
Ictidomys tridecemlineatus	ENSSTOG00000013216	1 retrocopy	retro_itri_1152,