RetrogeneDB ID: retro_cjac_3197

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:21286642..21287191(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM76A
• Ensembl ID: ENSCJAG00000009327
• Aliases: None
• Description: family with sequence similarity 76, member A [Source:HGNC Symbol;Acc:28530]

Sequence

>retro_cjac_3197
TGCTGGCTGTGCACACTTTCATACAAGCGGGTCCTTCAGAAGACCAAAGAGCAGAGGAAACACCTGAGTAGCTCTTCTCG
TGCTGACCACCAGGAGAAGGAGCAGTATAGTCGCCTGAGTGGTGGTGGCCATTATAACAGCCAGAAAACACTTTCTACAT
ATTCAACTCAAAATGAAATCCCAAAGAAAAAGTCCACGTTTGAGTCAATCACAACTAATGGAGACAGCTTCTCCCCAGAC
CTGGCTCTGGACTCACCAGACACTGACCACTTTGTCATCATTGCCTAACTGAAGGAAGAAGTAGCTACCCTAAAGAAGAT
GTTGCATCAAAAGGATCAAATGATTTTAGAGAAAGAGAAGAAGATTACAGAGGTGAAGGCTGATTTTCAGTACCAGGAAT
CACAGATGAGAGCCAAAATGAACCAGATGGAGAAAACCGACAAAGAAGTCACAGAACAATTGCAGGCCAAAAACCGAGAG
CTCCTGAATCAGGCAGCTGCCTTGTCCGAGAGCAAGAAGTCAGAGAAGTCAGGAGCTATAACCTCTCCG

Alignment

ORF - retro_cjac_3197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.54 %
• Parental protein coverage: 59.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CWLCTLSYKRVLQKTKEQRKHLSSSSRAGHQEKEQYSRLSGGGHYNSQKTLSTSSIQNEIPKKKSKFESI
          CWLCTLSYKRVLQKTKEQRKHLSSSSRA.HQEKEQYSRLSGGGHYNSQKTLST.S.QNEIPKKKS.FESI
Retrocopy CWLCTLSYKRVLQKTKEQRKHLSSSSRADHQEKEQYSRLSGGGHYNSQKTLSTYSTQNEIPKKKSTFESI

Parental  TTNGDSFSPDLALDSPGTDHFVIIAQLKEEVATLKKMLHQKDQMILEKEKKITELKADFQYQESQMRAKM
          TTNGDSFSPDLALDSP.TDHFVIIA.LKEEVATLKKMLHQKDQMILEKEKKITE.KADFQYQESQMRAKM
Retrocopy TTNGDSFSPDLALDSPDTDHFVIIA*LKEEVATLKKMLHQKDQMILEKEKKITEVKADFQYQESQMRAKM

Parental  NQMEKTHKEVTEQLQAKNRELLKQAAALSKSKKSEKSGAITSP
          NQMEKT.KEVTEQLQAKNRELL.QAAALS.SKKSEKSGAITSP
Retrocopy NQMEKTDKEVTEQLQAKNRELLNQAAALSESKKSEKSGAITSP

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	0.24 RPM	10.16 RPM
SRP051959_heart	0.84 RPM	20.61 RPM
SRP051959_kidney	0.91 RPM	21.12 RPM
SRP051959_liver	0.35 RPM	9.99 RPM
SRP051959_lung	0.99 RPM	18.04 RPM
SRP051959_lymph_node	0.66 RPM	15.55 RPM
SRP051959_skeletal_muscle	0.90 RPM	22.60 RPM
SRP051959_spleen	0.57 RPM	17.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3197 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3197 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009327	1 retrocopy	retro_cjac_3197 ,
Mus musculus	ENSMUSG00000028878	2 retrocopies	retro_mmus_1689, retro_mmus_2783,
Ochotona princeps	ENSOPRG00000017049	1 retrocopy	retro_opri_911,