RetrogeneDB ID: retro_cjac_2695

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:18844643..18845650(+)
• Located in intron of: ENSCJAG00000012996

Retrocopy information

• Ensembl ID: ENSCJAG00000013008
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSNK1G3
• Ensembl ID: ENSCJAG00000017348
• Aliases: None
• Description: None

Sequence

>retro_cjac_2695
AAAGGGGACATGGAGGAGGGCCGGAGAATGTCCAAGGCTGGAGAGGGCCGGAGCAGCCACGGTATCCGGAGCGCGGGTAC
CAGCTCGAGGGTCCTGATGGTGGGCCCCAACTGCCGCGTCGGCAAGAAGATCGGCTGTGGCAACTTCCGGGAGCTCCGCC
TAGGAAAGAATCTTCATACAAATGAATACGTGGCTATCAAATTGGAGCCGATCAAGTCGCGGGCCCCACAGCTGCACCTG
GAGTACCGGTTCTACAAGCAGCTCAGTGCCACAGAGGGCGTCCCTCAGGTCTACTACTTCAGCCCCTTGGGAAGTACAAC
GCCATGGTGCTGGAGCTGCTGGGGCCCAGCCTGGAGGACCTGTTCAACCTGTGCGACTGGACCTTTATGCTCAAGACGGT
GCTGATGATCGCCATCCAGCTGATCACCCGCATGCAGTACATGCGCACCAAGAGCTTCATCTACCGGGATGTGAAGCTGA
GAACTTCCTGGTGGGCTGCCCGGGGACCAAGTGGAAGCACATCATCCCCGTCATCAGCTTCGGGCTGGCCAAGGAGTATA
TCGACCCTGACACCAAGAAGCACATCCCGTACTGTGAGCACAAGAGCCTGACAGCACGGCGGGCTTCATGAGCATCAACA
CGCAGCTGGGTGAGGAGCAGAGCCGCTGCAACAACCTGGAGGCGCTGGGCCACTTGTTCATGTACTTCCTGCGGGGCAGC
CTCCCCTGGCAGGGGGGCTCAAGGCCGACACGCCCAAGGAGCGGTACCAGAAGATCGGGGACACCAAAGGTGCCACGCCC
ATTGAGGTGCTGTGTGAGAACTTCCCAGAAAAGATGGCCACATACCTGCGCTATGTGCGGCGCCTGGACTTCTTCAAGAA
GCTGGACTATGACTACCTGCGCAAGCTCTTCACCGACCTCTTCGACTGCAGCGGCTTCGTGTTCGACTATGAGTACGACT
GGGCCGGGAAGCCCCTCCTGACCCCCATCGGCACTATCCACACCGAC

Alignment

ORF - retro_cjac_2695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.18 %
• Parental protein coverage: 75.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKDKDKSDDRMARPSGRSGHNTRGTGSSSSGVLMVGPNFRVGKKIGCGNFGELRLGKNLYTNEYVAIKLE
          K.D............GRS.H..R..G.SS..VLMVGPN.RVGKKIGCGNF.ELRLGKNL.TNEYVAIKLE
Retrocopy KGDMEEGRRMSKAGEGRSSHGIRSAGTSSR-VLMVGPNCRVGKKIGCGNFRELRLGKNLHTNEYVAIKLE

Parental  PMKSRAPQLHLEYRFYKQLGSGDGIPQVYYFG-PCGKYNAMVLELLGPSLEDLFDLCDRTFSLKTVLMIA
          P.KSRAPQLHLEYRFYKQL....G.PQVYYF..P.GKYNAMVLELLGPSLEDLF.LCD.TF.LKTVLMIA
Retrocopy PIKSRAPQLHLEYRFYKQLSATEGVPQVYYFS<PLGKYNAMVLELLGPSLEDLFNLCDWTFMLKTVLMIA

Parental  IQLISRMEYVHSKNLIYRDVK-PENFLIGRPGNKTQQVIHIIDFGLAKEYIDPETKKHIPYREHKSLT-G
          IQLI.RM.Y...K..IYRDVK..ENFL.G.PG.K....I..I.FGLAKEYIDP.TKKHIPY.EHKSLT..
Retrocopy IQLITRMQYMRTKSFIYRDVK<AENFLVGCPGTKWKHIIPVISFGLAKEYIDPDTKKHIPYCEHKSLT<S

Parental  TARYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLPWQGLKADTL-KERYQKIGDTKRATPI-EVLCEN
          TA..MSINT.LG.EQSR...LEALGH.FMYFLRGSLPWQG....T.........G..K...P..EVLCEN
Retrocopy TAGFMSINTQLGEEQSRCNNLEALGHLFMYFLRGSLPWQGGSRPTRPRSGTRRSGTPKVPRPL<EVLCEN

Parental  FPE-MATYLRYVRRLDFFEKPDYDYLRKLFTDLFDRKGYMFDYEYDWIGKQLPTPVGAVQQD
          FPE.MATYLRYVRRLDFF.K.DYDYLRKLFTDLFD..G..FDYEYDW.GK.L.TP.G....D
Retrocopy FPEKMATYLRYVRRLDFFKKLDYDYLRKLFTDLFDCSGFVFDYEYDWAGKPLLTPIGTIHTD

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	0.49 RPM	21.63 RPM
SRP051959_heart	1.18 RPM	16.15 RPM
SRP051959_kidney	0.64 RPM	22.12 RPM
SRP051959_liver	0.39 RPM	8.82 RPM
SRP051959_lung	1.38 RPM	20.61 RPM
SRP051959_lymph_node	1.39 RPM	23.79 RPM
SRP051959_skeletal_muscle	1.35 RPM	6.97 RPM
SRP051959_spleen	1.01 RPM	26.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2695 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2695 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017550	1 retrocopy	retro_btau_1659,
Callithrix jacchus	ENSCJAG00000017348	2 retrocopies	retro_cjac_2695 , retro_cjac_3279,
Callithrix jacchus	ENSCJAG00000021121	1 retrocopy	retro_cjac_2680,
Macaca mulatta	ENSMMUG00000006646	1 retrocopy	retro_mmul_1040,
Mus musculus	ENSMUSG00000073563	1 retrocopy	retro_mmus_3454,
Otolemur garnettii	ENSOGAG00000011587	1 retrocopy	retro_ogar_246,
Rattus norvegicus	ENSRNOG00000016677	1 retrocopy	retro_rnor_2189,