RetrogeneDB ID: retro_cjac_2577

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:144386567..144386992(+)
• Located in intron of: ENSCJAG00000018570

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010374
• Aliases: None
• Description: None

Sequence

>retro_cjac_2577
CAAACTTATATGGAAACAAATTCTGTAGAACGTGTTCAAGTAAAACAAGGAGACCAAAGAAAGGGTAAGCAAGATATAGT
AGAAAAGTTAAAAGAAAATCGGTCTTTGCAGACATAAGCAGCATCTTAAGAGAACTTATTTAAGAGAGAATAAAGTTGCT
TCAATAAGAAGTCGGAGGGAGCTGAGAAAGATCTGAAATCTGAACTCTTGAAAATGAAAACTTTCCACAAGACTAATCAA
ACTGACTTGGAAAGATATAAGCAGCTCTATCTACAAGAATTTAAAGTCAGAAAATCATTGGCAACTATACTAAACAAAAC
CAATGATAAAACAGCAGAGGTTAAGAGCAAACTTTTTGTAGAGAACAGCAGATCAGATCTTTACACCACTGTTACTACGA
GGCAGTCCTAGCGTCAGCTTGTGTG

Alignment

ORF - retro_cjac_2577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.29 %
• Parental protein coverage: 54.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSHLERNMVERGQVKQYKQEIEERARQEIVEKLKEVNLFLQAQAASQENLEQLRENSFASMKSQMELRIN
          ....E.N.VER.QVKQ..Q.......Q.IVEKLKE.N..LQ..AAS.ENL...RE.S....KS.......
Retrocopy QTYMETNSVERVQVKQGDQR---KGKQDIVEKLKE-NRSLQT*AAS*ENLFK-RE*SCFNKKSEGAEK--

Parental  DLESELSKMKTFQEDVNKTELEKYKQLYLEELKVRKSLSNKLNKTNERLAEVNTKLLMEKQQTRSLFTTL
          DL.SEL.KMKTF....N.T.LE.YKQLYL.E.KVRKSL...LNKTN...AEV..KL..E......L.TT.
Retrocopy DLKSELLKMKTFHK-TNQTDLERYKQLYLQEFKVRKSLATILNKTNDKTAEVKSKLFVENSRS-DLYTTV

Parental  TTR-PVLVSPCV
          TTR..VL.S.CV
Retrocopy TTR<AVLASACV

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	0.29 RPM	0.11 RPM
SRP051959_heart	0.26 RPM	0.09 RPM
SRP051959_kidney	0.13 RPM	0.04 RPM
SRP051959_liver	0.02 RPM	0.11 RPM
SRP051959_lung	0.23 RPM	0.13 RPM
SRP051959_lymph_node	0.25 RPM	0.14 RPM
SRP051959_skeletal_muscle	0.11 RPM	0.07 RPM
SRP051959_spleen	0.25 RPM	0.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2577 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2577 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010374	1 retrocopy	retro_cjac_2577 ,
Gorilla gorilla	ENSGGOG00000027866	1 retrocopy	retro_ggor_2191,