RetrogeneDB ID: retro_cjac_671

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:29695910..29696704(+)
• Located in intron of: ENSCJAG00000000894

Retrocopy information

• Ensembl ID: ENSCJAG00000000923
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK1
• Ensembl ID: ENSCJAG00000007001
• Aliases: None
• Description: cyclin-dependent kinase 1 [Source:HGNC Symbol;Acc:1722]

Sequence

>retro_cjac_671
ATGGAAGATTATACTAAAATAGAGAAAATTGGAGAAGGTACCTATGGAGTTGTGTATAAAGGTAGACACAAAACTACAGG
TCAAGTGGTCACCATGAAAAAAATCAGACTAGAAAGTGAAGAGGAAGGGGTTCCTAGTACTGCGATTCGGGAAATTTCTC
TATTAAAAGAACTTCGTCATCTAAATATAGTCAGTCTTCAGGATGTGCTTATGCAGGATTCCAGGTTATATCTCATCTTT
GAATTTCTTTCCATGGATCTGAAGAAATACTTAGATTCTATCCCTCCTGGCCAATACATGGATTCTTCACTTGTTAAGAG
TTATTTAACCAAATCCTACAGGGGATTGTGTTTTGTCACTCTAGAAGAGTTCTTCACAGAGACTTAAAACCTCAAAATCT
CTTGATTGATGACAAAGGAACAATTAAACTGGCTGATTTTGGCCTTGCCAGAGCTTCTGGAATACCTATTAGAGTATATA
CACATGAGGTAGTGACACTCTGGTACAGATCACCAGAAGTATTGCTGGGGTCAGCTCGTTACTCGACTCCAGTTGATATT
TGGAGTATAGGCACCATATTTGCTGAACTAGCAACTAAGAAACCACTTTTCCATGGGGATTCAGAAATTGATCAACTCTT
CAGGATTTTCAGAGCTTTGGGCACTCCTAATAATGAAGTCCGGCCAGAAGTGGAATACTTACGGGACTATAAGAATACAT
TTCCCAAGTGGAAACCAGGAAGCCTAGCATCCCATGTCAAAAACTTGGATGAAAATGACTTGGATTTGCTCTCA

Alignment

ORF - retro_cjac_671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.85 %
• Parental protein coverage: 89.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEDYTKIEKIGEGEWLYYYTHNHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVL
          MEDYTKIEKIGEG.....Y...HKTTGQVV.MKKIRLESEEEGVPSTAIREISLLKELRH.NIVSLQDVL
Retrocopy MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVTMKKIRLESEEEGVPSTAIREISLLKELRHLNIVSLQDVL

Parental  MQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKVKAYSYLYQ-ILQGIVFCHSRRVLHRDLKPQNLL
          MQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVK....SYL...ILQGIVFCHSRRVLHRDLKPQNLL
Retrocopy MQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVK----SYLTK<ILQGIVFCHSRRVLHRDLKPQNLL

Parental  IDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFH
          IDDKGTIKLADFGLARA.GIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFH
Retrocopy IDDKGTIKLADFGLARASGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFH

Parental  GDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLS
          GDSEIDQLFRIFRALGTPNNEV.PEVE.L.DYKNTFPKWKPGSLASHVKNLDEN.LDLLS
Retrocopy GDSEIDQLFRIFRALGTPNNEVRPEVEYLRDYKNTFPKWKPGSLASHVKNLDENDLDLLS

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	2.15 RPM	9.67 RPM
SRP051959_heart	0.70 RPM	0.12 RPM
SRP051959_kidney	0.58 RPM	0.98 RPM
SRP051959_liver	0.13 RPM	0.54 RPM
SRP051959_lung	0.65 RPM	1.43 RPM
SRP051959_lymph_node	1.58 RPM	3.45 RPM
SRP051959_skeletal_muscle	0.44 RPM	0.00 RPM
SRP051959_spleen	1.58 RPM	3.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_671 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_671 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671 ,
Callithrix jacchus	ENSCJAG00000012261	1 retrocopy	retro_cjac_961,
Callithrix jacchus	ENSCJAG00000014175	1 retrocopy	retro_cjac_4070,
Callithrix jacchus	ENSCJAG00000020258	1 retrocopy	retro_cjac_1522,
Cavia porcellus	ENSCPOG00000005402	3 retrocopies	retro_cpor_1414, retro_cpor_1422, retro_cpor_200,
Dasypus novemcinctus	ENSDNOG00000018590	1 retrocopy	retro_dnov_265,
Equus caballus	ENSECAG00000009716	1 retrocopy	retro_ecab_637,
Felis catus	ENSFCAG00000014972	1 retrocopy	retro_fcat_329,
Microcebus murinus	ENSMICG00000005793	1 retrocopy	retro_mmur_43,
Monodelphis domestica	ENSMODG00000017091	1 retrocopy	retro_mdom_702,
Rattus norvegicus	ENSRNOG00000000632	1 retrocopy	retro_rnor_1638,
Tupaia belangeri	ENSTBEG00000017549	3 retrocopies	retro_tbel_3309, retro_tbel_807, retro_tbel_812,
Tursiops truncatus	ENSTTRG00000001085	2 retrocopies	retro_ttru_1619, retro_ttru_1634,