RetrogeneDB ID: retro_cjac_1522

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:72026008..72026879(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013768
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK5
• Ensembl ID: ENSCJAG00000020258
• Aliases: None
• Description: cyclin-dependent kinase 5 [Source:HGNC Symbol;Acc:1774]

Sequence

>retro_cjac_1522
ATGCAGAAATATAAAAAACTGGAAAAGATTGGGGAAGGCACCTGCTGGACATTGTTCAAGGCCAAAAACTGGGAGACTCA
TGAGATCGTGGCTCTGAAACAGGTGAGGCTGGATGACGATGCTGAGGCTGTGCCGAGTTCCGCCCTCTGGGAGTTCTGCC
TACTCATGGAGCTGAAGCACAAGAACGTCATCAGGCTTCATGACATCCTGCACAGCAACGAGAAGCTGACTTTGGTTTTT
GAATTCTGTGACCAGGACCTGAAGAAGTATTTTGACAAGTGCAATGGTGACCTTGACCTTGAGATTGTAAAGTCCTTCCT
CCTCCAGCTGCTAAAGGCCTGGGATTCTGTCACAGCCGCAATGTGGTACACAGGGACCTGAAGCCCCAGAATCTGCTAAT
GAACAGGAATGGGGAACTACAATTGGCTGATTTTGGCCCGGCTCAAGCCTTTGGGATCCCCGTCCGCTGTTACTCAGCTG
GGGTGGTCACACTGTGGTACCACCCACCAGATGTCCTCTTTCAGGCCAAGTTGTACTCCACAGCCATCAACATGTATCAG
CCGGCTGCATCTTTGCAAAACTGGCCAATGCTGGGTGGCCTCTTTTTCCTGGCAATGATGTCGATGAACAGTTGAAGAGG
ATCTTCCGGCTGCTGGAGACACCCACTGAGGAGCAGTGGCCCTCCACGACCAAGCTGCCAGACTACAAGCCCTACCCAGT
GTACCCAGACACAACATCCCTGGTGAACATCGTGCCCAAAGTCAATGCCACAGGGAGGCATCCGCTGCAGAATCTTCTGA
CATGTAACCCTGTCCAACATATCTCAGCAGAAGAGGCCCCACAGCACCCCTACTTCTCCAACTTCTGTCCA

Alignment

ORF - retro_cjac_1522 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.96 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVL
          MQKY.KLEKIGEGT..T.FKAKN.ETHEIVALK.VRLDDD.E.VPSSAL.E.CLL.ELKHKN..RLHD.L
Retrocopy MQKYKKLEKIGEGTCWTLFKAKNWETHEIVALKQVRLDDDAEAVPSSALWEFCLLMELKHKNVIRLHDIL

Parental  HSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLK-GLGFCHSRNVLHRDLKPQNLLINRNGE
          HS..KLTLVFEFCDQDLKKYFD.CNGDLD.EIVKSFL.QLLK.GLGFCHSRNV.HRDLKPQNLL.NRNGE
Retrocopy HSNEKLTLVFEFCDQDLKKYFDKCNGDLDLEIVKSFLLQLLK<GLGFCHSRNVVHRDLKPQNLLMNRNGE

Parental  LKLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMW-SAGCIFAELANAGRPLFPGNDV
          L.LADFG.A.AFGIPVRCYSA.VVTLWY.PPDVLF.AKLYST.I.M..SAGCIFA.LANAG.PLFPGNDV
Retrocopy LQLADFGPAQAFGIPVRCYSAGVVTLWYHPPDVLFQAKLYSTAINMY<SAGCIFAKLANAGWPLFPGNDV

Parental  DDQLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAE
          D.QLKRIFRLL.TPTEEQWPS.TKLPDYKPYP.YP.TTSLVN.VPK.NATGR..LQNLL.CNPVQ.ISAE
Retrocopy DEQLKRIFRLLETPTEEQWPSTTKLPDYKPYPVYPDTTSLVNIVPKVNATGRHPLQNLLTCNPVQHISAE

Parental  EALQHPYFSDFCP
          EA.QHPYFS.FCP
Retrocopy EAPQHPYFSNFCP

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	2.64 RPM
SRP051959_heart	0.00 RPM	2.67 RPM
SRP051959_kidney	0.00 RPM	4.46 RPM
SRP051959_liver	0.00 RPM	3.03 RPM
SRP051959_lung	0.00 RPM	3.24 RPM
SRP051959_lymph_node	0.00 RPM	3.45 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.77 RPM
SRP051959_spleen	0.00 RPM	3.80 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1522 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1522 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1522 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 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 ,
Homo sapiens	ENSG00000164885	1 retrocopy	retro_hsap_4002,
Gorilla gorilla	ENSGGOG00000016879	1 retrocopy	retro_ggor_2686,
Nomascus leucogenys	ENSNLEG00000004100	1 retrocopy	retro_nleu_549,
Pongo abelii	ENSPPYG00000018183	1 retrocopy	retro_pabe_3290,
Pan troglodytes	ENSPTRG00000019872	1 retrocopy	retro_ptro_2717,
Ictidomys tridecemlineatus	ENSSTOG00000016068	1 retrocopy	retro_itri_906,