RetrogeneDB ID: retro_cjac_581

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:86591592..86592228(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TNNI3
• Ensembl ID: ENSCJAG00000017677
• Aliases: None
• Description: troponin I type 3 (cardiac) [Source:HGNC Symbol;Acc:11947]

Sequence

>retro_cjac_581
ATGGGGGAGGAGAGCAGCCATGCGGCTGGGGAACCTCGCTCCGCACCAGCCCCGGTCAGACGCCGCTCCTCCAACTACCG
CGCGCGTACGCCACGGAGCCTCATGCCAAGAAAAAGTCTAAGATGTCCGTCCGCCTCGAGAAAACTGCAGCTGAAGACCC
TGATGCTGCAGATTGCAAAGCAGGAGCTGGAGCGAGAGGCGGAGGAGCTGCGCGGAGAGAAGGGCGCGCCCTGAGCACCC
GCTGCCAGCCGCTGCAGTTGGCCGGTCTAGCCTTCGCGGAGCTGCAGGACTTGTGCCGACAGCTCCACACCCGTGTGGAC
AAAGTGGATGAAGAGAGATATGACCTAGAGGCAAGAGATACCAAGAACATCACAGAGATTGCAGATCTGACCCAGAAGAT
CTTCGACCTTCGTGGCAAGTTTAAGCGGCCCACCCTGCAGGAGAGTGAGAATCTCTGCGGATGCCATGATGCAGGCGCTG
CTGGGGACCCAGGCTAAGGAGTCCCTGGACCTGCGTGCCCACCTCAAGTAGGTGAAGAAGGAGGACACCGAGAAGGAAAT
CCGGGAGGTGGGAGACTGGCGCAAGAACATCAATGCACTGAGTGGAATGGAAGGCCACAAGAAAAAGTTTGAGGGC

Alignment

ORF - retro_cjac_581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADESSDAAGEPRPAPAPVRRRSSNYRAYATEPHAKKKSKI--SASRKLQLKTLMLQIAKQELEREAEER
          M..ESS.AAGEPR.APAPVRRRSSNYRA.........KS....SASRKLQLKTLMLQIAKQELEREAEE.
Retrocopy MGEESSHAAGEPRSAPAPVRRRSSNYRARTPRSLMPRKSLRCPSASRKLQLKTLMLQIAKQELEREAEEL

Parental  RGEKG-RALSTRCQPLELAGLGFAELQDLCRQLHTRVDKVDEERYDIEAKVTKNITEIADLTQKIFDLRG
          RGEKG.RALSTRCQPL.LAGL.FAELQDLCRQLHTRVDKVDEERYD.EA..TKNITEIADLTQKIFDLRG
Retrocopy RGEKG<RALSTRCQPLQLAGLAFAELQDLCRQLHTRVDKVDEERYDLEARDTKNITEIADLTQKIFDLRG

Parental  KFKRPTL-RRVRISADAMMQALLGTRAKESLDLRAHLKQVKKEDTEKEIREVGDWRKNIDALSGMEGRKK
          KFKRPTL.RRVRISADAMMQALLGT.AKESLDLRAHLK.VKKEDTEKEIREVGDWRKNI.ALSGMEG.KK
Retrocopy KFKRPTL>RRVRISADAMMQALLGTQAKESLDLRAHLK*VKKEDTEKEIREVGDWRKNINALSGMEGHKK

Parental  KFEG
          KFEG
Retrocopy KFEG

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	0.20 RPM
SRP051959_heart	0.32 RPM	415.51 RPM
SRP051959_kidney	0.00 RPM	0.82 RPM
SRP051959_liver	0.00 RPM	0.11 RPM
SRP051959_lung	0.00 RPM	6.72 RPM
SRP051959_lymph_node	0.00 RPM	0.98 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.92 RPM
SRP051959_spleen	0.00 RPM	0.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_581 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_581 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_581 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017677	1 retrocopy	retro_cjac_581 ,