RetrogeneDB ID: retro_cjac_2030

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:31475970..31476391(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP2
• Ensembl ID: ENSCJAG00000018124
• Aliases: None
• Description: FK506 binding protein 2, 13kDa [Source:HGNC Symbol;Acc:3718]

Sequence

>retro_cjac_2030
ATGAGGCTGAGCTGGGCCCAGGTCCTGACAGTACTGTCCATCCGCCTGAGCGCTGTGGCCACAGCCACGGGGCCGAGGGC
AAAAGGAAGCTGCAGATCCGAGTCAAGAAGCGGGTGGACCACTGTCCCATTAAATCTCGTAAAGGCTATGTCCTGCACTT
GCACTACACGGGGAAGCTGGAAGATGGGACGGAGTTTGATAGCAGCCTGTCCCCGAGCCAGCCCTTTGTCTTCTCCCTTG
GCACAGGCCAGGTCATCAAGGGCTGGGTCCAGGGGCTGCTGGGGATGTGTGAGGGGGAAAGTTCAAGCTGGTGATCCCAT
CCGAGCTGGCGTATGGAGAGCGGGGAGCTCCCCCAAAGATTCCAGGCGGTGCAACCCTGGTGTTCCAGGTGGAGCTGCTC
AAAATTTAGCAACGATCCGAT

Alignment

ORF - retro_cjac_2030 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.31 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRLSWVQVLTVLSICLSAVATATG-AEGKRKLQIGVKKRVDHCPIKSRKGDVLHMHYTGKLEDGTEFDSS
          MRLSW.QVLTVLSI.LSAVATATG.AEGKRKLQI.VKKRVDHCPIKSRKG.VLH.HYTGKLEDGTEFDSS
Retrocopy MRLSWAQVLTVLSIRLSAVATATG<AEGKRKLQIRVKKRVDHCPIKSRKGYVLHLHYTGKLEDGTEFDSS

Parental  L--PQPFVFSLGTGEVIKGWDQGLLGMCEAEKS-KLVIPSKLGYGELGAPPKIPGGATLVFEVELLKIER
          L...QPFVFSLGTG.VIKGW.QGLLGMCE.E.S.KLVIPS.L.YGE.GAPPKIPGGATLVF.VELLKI..
Retrocopy LSPSQPFVFSLGTGQVIKGWVQGLLGMCEGESS<KLVIPSELAYGERGAPPKIPGGATLVFQVELLKI*Q

Parental  RSE
          RS.
Retrocopy RSD

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	5.92 RPM
SRP051959_heart	0.18 RPM	7.56 RPM
SRP051959_kidney	0.22 RPM	12.14 RPM
SRP051959_liver	0.26 RPM	10.27 RPM
SRP051959_lung	0.15 RPM	8.70 RPM
SRP051959_lymph_node	0.16 RPM	7.94 RPM
SRP051959_skeletal_muscle	0.04 RPM	4.76 RPM
SRP051959_spleen	0.23 RPM	10.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2030 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2030 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2030 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000758	1 retrocopy	retro_acar_126,
Bos taurus	ENSBTAG00000013606	3 retrocopies	retro_btau_1418, retro_btau_69, retro_btau_916,
Callithrix jacchus	ENSCJAG00000018124	2 retrocopies	retro_cjac_2030 , retro_cjac_3853,
Cavia porcellus	ENSCPOG00000002928	1 retrocopy	retro_cpor_39,
Macaca mulatta	ENSMMUG00000012945	1 retrocopy	retro_mmul_1397,
Rattus norvegicus	ENSRNOG00000021153	1 retrocopy	retro_rnor_1034,