RetrogeneDB ID: retro_cjac_2342

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:61789479..61790040(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000001758
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000018827
• Aliases: None
• Description: None

Sequence

>retro_cjac_2342
AAGGAGCTGCCTGCCCTTCCAACAGCCACCCTACTGGATCTATCTTTTAATAAACTGACTATTCTACCTTCGGATTTCTG
TGGCCTCACACACCTGGCGAAGCTAGACCTGAGGAAGAACAAGCCACAGCAGCTGCGGGGCGGACTTCAGGGGTCTGGTC
GACCTCCAGCACCTGGCTCTCCTCAACAACAGGCTGTCACCTGTCAGCCCTGCTCAGCTCAACAACCGGAAGTGGCTGCA
CCGGAAGGATGATCCCCCGAGTCCCGGCTGGGCCTCCGCGGCAGGCGGCTGCTTGGGTGAGAAGCAGTGGAAGCAGTGTG
CCAACAAGGCGCCACAGCGGGCCAAGCAGGCAGTCAGGAGCTGGAGAGGCAGCGGGCCTGGAAGTAAGCAGAACGAGAGG
CGGAGGAGAAGCCTGAGGCCAAGCAGCGAGCTAAGGAAGCTCGGGAGAGGGAACTGTGGAAGCGAGAGAAGGAGGAAGAG
AAGGAGCGCCGGAAAAAGGAGTATGATGCCCTCAAAGCAGCCAAGCGGCAGCAGAAGAAACCAACGAAGGAAACAAATCA
G

Alignment

ORF - retro_cjac_2342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.62 %
• Parental protein coverage: 62.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KELAALPKATILDLSCNKLTTLPSDFCGLTHLVKLDLSKNKLQQLP-ADFGRLVNLQHLDLLNNRLVTLP
          KEL.ALP.AT.LDLS.NKLT.LPSDFCGLTHL.KLDL.KNK.QQL..ADF..LV.LQHL.LLNNRL...P
Retrocopy KELPALPTATLLDLSFNKLTILPSDFCGLTHLAKLDLRKNKPQQLR>ADFRGLVDLQHLALLNNRLS--P

Parental  VSFARLKNLKWLDLKDNPLDPVLAKVAGDCLDEKQCKQCANKVLQHMKAVQA-DQERERQRRLE-VEREA
          VS.A.L.N.KWL..KD.P..P..A..AG.CL.EKQ.KQCANK..Q...A.QA..QE.ERQR.....EREA
Retrocopy VSPAQLNNRKWLHRKDDPPSPGWASAAGGCLGEKQWKQCANKAPQ--RAKQA<SQELERQRAWK*AEREA

Parental  EKKREAKQRAKEAQERELRKREKAEEKERRRKEYDALKAAKREQEKKPKKEANQ
          E.K.EAKQRAKEA.EREL.KREK.EEKERR.KEYDALKAAKR.Q.KKP.KE.NQ
Retrocopy EEKPEAKQRAKEARERELWKREKEEEKERRKKEYDALKAAKR-QQKKPTKETNQ

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	20.41 RPM
SRP051959_heart	0.00 RPM	6.89 RPM
SRP051959_kidney	0.09 RPM	9.94 RPM
SRP051959_liver	0.39 RPM	13.41 RPM
SRP051959_lung	0.00 RPM	8.18 RPM
SRP051959_lymph_node	0.00 RPM	7.12 RPM
SRP051959_skeletal_muscle	0.07 RPM	5.50 RPM
SRP051959_spleen	0.00 RPM	10.59 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_cjac_2342 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
HX599653	61789561	61789712	98.1	148	3	145
HX629901	61789561	61789712	98.1	148	3	145

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2342 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018827	1 retrocopy	retro_cjac_2342 ,
Equus caballus	ENSECAG00000018072	1 retrocopy	retro_ecab_240,
Homo sapiens	ENSG00000108829	1 retrocopy	retro_hsap_3479,
Gorilla gorilla	ENSGGOG00000006310	1 retrocopy	retro_ggor_2346,
Monodelphis domestica	ENSMODG00000020901	1 retrocopy	retro_mdom_1882,
Nomascus leucogenys	ENSNLEG00000009066	1 retrocopy	retro_nleu_2629,
Pongo abelii	ENSPPYG00000008284	3 retrocopies	retro_pabe_2687, retro_pabe_2874, retro_pabe_2875,
Pan troglodytes	ENSPTRG00000009398	1 retrocopy	retro_ptro_2985,
Tarsius syrichta	ENSTSYG00000000371	1 retrocopy	retro_tsyr_25,
Tursiops truncatus	ENSTTRG00000000207	1 retrocopy	retro_ttru_1931,