RetrogeneDB ID: retro_cjac_2680

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:150316394..150317396(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000018001
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSNK1A1
• Ensembl ID: ENSCJAG00000021121
• Aliases: None
• Description: casein kinase 1, alpha 1 [Source:HGNC Symbol;Acc:2451]

Sequence

>retro_cjac_2680
ATGATGAAAAACAGCGGCTCCAAGGCCGAGCTCATTGTGGGAGGGAAATACAAACTGGTGCGGAAGATCGGGTCTGGCTC
CTTCGGAGACGTTTATCTGGGAATCGCCACCAGCAACGGGGAGGAAGTGGCAGTGAAGCTGGAATCTCAGAAGGCCAAGC
ACCCGCAGCTGCTGTATGAGAGCAGACTCTACACGATTCTTCAGGGTGGGACTGGCATCCCCCACATGCACTGGTATGGC
CAGGAAAAAGACAGCAATGTGCTAGTCATGGACCTTCTGGGGCCCAGCCTCGAAGACCTCTTTAATTTCTGTTCCAGAAG
GTTCACCATGAAAACTGTACTTATGTTAGCCGACCAGATGATCAGTAGAATTGAATACGTGCATACGATGAGTTTTCTAC
ACCGAGACATTAAACCAGATAACTTCCTGATGGGTACTGGGCGTCACTGTAATAAGCTGTTCCTTATTGATTTTGGTTTG
GCCAAAAGGTACAGAGACAACAGGACTAGGCAACACATCCCGTACAGAGAAGATAAACACCTCATTGGCACTGTCCGATA
TGCCAGCATCAATGCACATCTTGGTATTGAGCAGAGCCGCCGAGATGACATGGAATCCTTAGGCTACGTTTTCATGTATT
TTAATAGAACCAACCTGCCGTGGCAAGGACTAAAGGCTATGACAAAGAAACAAAAATACGACAAGATTAGTGAGAAGAAG
ATGTCCACGCCTGTTGAAGTTTTATGTAAGGGATTTCCTGCGGAATTTGCCATGTACTTGAATTACTGTCGTGGGCTGCG
CTTTGAGGAAGTCCCAGATTACACGTATCTGAGGCAGCTCTTCCGCATTCTTTTCAGGACCCTGAACCACCAATATGACT
ACACGTTTGACTGGATGATGTTAAAACAGAAAGCAGCACAGCAGGCAGCCTCTTCCAGTGGGCAGGGTCAGCAGGCTCAA
GCCCAGACAGGCAGTAAAACGAATAAAAAGGATAATGTGAAA

Alignment

ORF - retro_cjac_2680 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.36 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSSGSKAEFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKILQGG
          M...SGSKAE.IVGGKYKLVRKIGSGSFGD.YL.I...NGEEVAVKLESQKA.HPQLLYES.LY.ILQGG
Retrocopy MMKNSGSKAELIVGGKYKLVRKIGSGSFGDVYLGIATSNGEEVAVKLESQKAKHPQLLYESRLYTILQGG

Parental  VGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPD
          .GIPH..WYGQEKD.NVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHT..F.HRDIKPD
Retrocopy TGIPHMHWYGQEKDSNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTMSFLHRDIKPD

Parental  NFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYV
          NFLMG.GRHCNKLFLIDFGLAK.YRDNRTRQHIPYREDK.L.GT.RYASINAHLGIEQSRRDDMESLGYV
Retrocopy NFLMGTGRHCNKLFLIDFGLAKRYRDNRTRQHIPYREDKHLIGTVRYASINAHLGIEQSRRDDMESLGYV

Parental  LMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQL
          .MYFNRT.LPWQGLKA.TKKQKY.KISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEE.PDY.YLRQL
Retrocopy FMYFNRTNLPWQGLKAMTKKQKYDKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEVPDYTYLRQL

Parental  FRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTPTGKQTDKTKSNMK
          FRILFRTLNHQYDYTFDW.MLKQKAAQQAASSSGQGQQAQ..TG..T.K.K.N.K
Retrocopy FRILFRTLNHQYDYTFDWMMLKQKAAQQAASSSGQGQQAQAQTGSKTNK-KDNVK

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	134.12 RPM
SRP051959_heart	0.09 RPM	129.52 RPM
SRP051959_kidney	0.11 RPM	96.75 RPM
SRP051959_liver	0.00 RPM	73.69 RPM
SRP051959_lung	0.05 RPM	101.95 RPM
SRP051959_lymph_node	0.07 RPM	87.58 RPM
SRP051959_skeletal_muscle	0.04 RPM	92.66 RPM
SRP051959_spleen	0.04 RPM	99.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2680 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2680 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_32
Pan troglodytes	retro_ptro_7
Gorilla gorilla	retro_ggor_984
Pongo abelii	retro_pabe_170
Macaca mulatta	retro_mmul_295

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005326	2 retrocopies	retro_btau_1662, retro_btau_49,
Canis familiaris	ENSCAFG00000018286	1 retrocopy	retro_cfam_1887,
Callithrix jacchus	ENSCJAG00000017348	2 retrocopies	retro_cjac_2695, retro_cjac_3279,
Callithrix jacchus	ENSCJAG00000021121	1 retrocopy	retro_cjac_2680 ,
Homo sapiens	ENSG00000113712	1 retrocopy	retro_hsap_32,
Gorilla gorilla	ENSGGOG00000013926	3 retrocopies	retro_ggor_1178, retro_ggor_742, retro_ggor_984,
Myotis lucifugus	ENSMLUG00000002910	4 retrocopies	retro_mluc_1531, retro_mluc_2134, retro_mluc_2215, retro_mluc_597,
Macaca mulatta	ENSMMUG00000001758	2 retrocopies	retro_mmul_2207, retro_mmul_295,
Monodelphis domestica	ENSMODG00000009937	1 retrocopy	retro_mdom_2005,
Oryctolagus cuniculus	ENSOCUG00000006669	7 retrocopies	retro_ocun_1068, retro_ocun_1098, retro_ocun_1506, retro_ocun_500, retro_ocun_502, retro_ocun_506, retro_ocun_644,
Sorex araneus	ENSSARG00000011446	1 retrocopy	retro_sara_518,
Sarcophilus harrisii	ENSSHAG00000015356	1 retrocopy	retro_shar_834,
Sus scrofa	ENSSSCG00000014435	1 retrocopy	retro_sscr_560,
Ictidomys tridecemlineatus	ENSSTOG00000022141	1 retrocopy	retro_itri_1378,
Drosophila melanogaster	FBgn0015024	4 retrocopies	retro_dmel_10, retro_dmel_32, retro_dmel_40, retro_dmel_67,