RetrogeneDB ID: retro_cjac_4079

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:66038579..66039011(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000010604
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNBP
• Ensembl ID: ENSCJAG00000017430
• Aliases: None
• Description: CCHC-type zinc finger, nucleic acid binding protein [Source:HGNC Symbol;Acc:13164]

Sequence

>retro_cjac_4079
GGGAGAGGAGACAGAGGCCATGGCAGAGGTTCTCAATGCAGTTCCACCACCCTATCATACACCTGTTACCGCTGCGGTGA
GTCTGGTCATCAAGCTAAGAACTGTGTCCTCGGAAACATCTGCTACAACTGTGGGAGAAGCGGCCACATCGCCAAAGACT
GTAACGAACCTAAACGAGAGAGAGACCAATGCTGTTATACCTGCGGCAGACCAGGACATCTGGCTTGTGACTGTGATCGT
CGCAAAGAGCAGAAATGCTACGTTTGTGGCAAACTTGGGCACATTCAGAAAGACTGCGCCGAGGTCAAGTGCTACAGATG
TGGCGAGACCGGCCACATGGCCATCAGTTGCAGCAAGGCGATCCAAGTCAACTGCTTCCGCTGTGGCAAATCCGGACACC
TAGCCAGGGAATGTTCTAGTGAGGCTACCGCT

Alignment

ORF - retro_cjac_4079 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.86 %
• Parental protein coverage: 82.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQEDEACYNCGRGGHIAKDCKEPKREREQCCYNC
          GRG.....RG.Q..S..L...CYRCGESGH.AK.C.L.....CYNCGR.GHIAKDC.EPKRER.QCCY.C
Retrocopy GRGDRGHGRGSQCSSTTLSYTCYRCGESGHQAKNCVL--GNICYNCGRSGHIAKDCNEPKRERDQCCYTC

Parental  GKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLAREC
          G.PGHLA.DCD...EQKCY.CG..GHIQKDC..VKCYRCGETGH.AI.CSK...VNC.RCG.SGHLAREC
Retrocopy GRPGHLACDCDRRKEQKCYVCGKLGHIQKDCAEVKCYRCGETGHMAISCSKAIQVNCFRCGKSGHLAREC

Parental  TIEATA
          ..EATA
Retrocopy SSEATA

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	44.86 RPM
SRP051959_heart	0.02 RPM	120.47 RPM
SRP051959_kidney	0.00 RPM	94.22 RPM
SRP051959_liver	0.00 RPM	93.66 RPM
SRP051959_lung	0.00 RPM	77.24 RPM
SRP051959_lymph_node	0.00 RPM	73.88 RPM
SRP051959_skeletal_muscle	0.00 RPM	206.28 RPM
SRP051959_spleen	0.00 RPM	81.70 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4079 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4079 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4079 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012159	1 retrocopy	retro_btau_19,
Callithrix jacchus	ENSCJAG00000017430	1 retrocopy	retro_cjac_4079 ,
Equus caballus	ENSECAG00000009512	1 retrocopy	retro_ecab_1072,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001,
Loxodonta africana	ENSLAFG00000002502	1 retrocopy	retro_lafr_49,
Oryctolagus cuniculus	ENSOCUG00000008696	2 retrocopies	retro_ocun_1626, retro_ocun_208,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Pteropus vampyrus	ENSPVAG00000015070	1 retrocopy	retro_pvam_908,
Sorex araneus	ENSSARG00000011874	1 retrocopy	retro_sara_397,
Sarcophilus harrisii	ENSSHAG00000017132	1 retrocopy	retro_shar_666,