RetrogeneDB ID: retro_ptro_2717

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:121434840..121435716(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CDK5
• Ensembl ID: ENSPTRG00000019872
• Aliases: None
• Description: None

Sequence

>retro_ptro_2717
ATGCAGAAATAAAAGAAACTGGAGAAGATTGGGGAAGGCACCTATGGGACAGTGTTCAAGGCCAAAAACTGGGAGACTCA
TGAGATTGTGGCTCTGAAATGGGTGAGGCTGGATGACAATGATGAGGGTGTGCCGAGTTCTGCCCTCCGGGAGATCTGCC
TACTCAAGGAGCTGAAGCACAAGAACATCGTCAGGCTTCATGACGTCCTGCACAGCGACAAGAAGCTGACTTTGGTTTTC
AAATTCTGTCACCAGCACCTGAAAAAGTATTTTGACAGTTGCAATGGTGACCTCGATCCTGAGATTGTAAAGTCATTTCT
CTTCCAGCTGCTAAAAGGCCTCGGATTCTGTCACAGCCGCAATGTGCTACGCAGGGACCTGAAGCCCCAGAACCTGCTAA
TAAACAGGAATGGGGAGCTGAAATTGGCTGACTTTGGCCTGTCTCGAGCCTTTGGGATCCCCATCTGCTGTTACTGAGCT
GGAGTGGTCACACTGTGGTACCACCCACCAGATGTCTTCTTTGGGGCCAAGCTGTACTCCACGTCCATTGACTTGTGGTC
AGCTGGCTGCATCTTTGCGGAGCTGGCCAATGCTGGATGGCCTCTTTTTCCAGGCAATGATGTCGATGACCAGTTGAAGA
GGATCTTCTGGCTGCTAGGGATGCTCACCAAGGAGCAGTGGCCCTCCATGACCAAGCTGCCAGACTATAAGCTGTACCCA
TTGTACCCGGCCACAACATCCCTGGTGAACATCGTGCCCAAACTCAATGCCACAGGGAGGGATCTGCTGCAGAATCTTCT
GAAGTGTAACCCCTGCCAATGTATCTCAGCAGAAGAGGCCCTGCAGCACCCCTACTTTTCCGACTTCTGTCCGCCC

Alignment

ORF - retro_ptro_2717 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVL
          MQK..KLEKIGEGTYGTVFKAKN.ETHEIVALK.VRLDD.DEGVPSSALREICLLKELKHKNIVRLHDVL
Retrocopy MQK*KKLEKIGEGTYGTVFKAKNWETHEIVALKWVRLDDNDEGVPSSALREICLLKELKHKNIVRLHDVL

Parental  HSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDLKPQNLLINRNGEL
          HSDKKLTLVF.FC.Q.LKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVL.RDLKPQNLLINRNGEL
Retrocopy HSDKKLTLVFKFCHQHLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLRRDLKPQNLLINRNGEL

Parental  KLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDD
          KLADFGL.RAFGIP..CY.A.VVTLWY.PPDV.FGAKLYSTSID.WSAGCIFAELANAG.PLFPGNDVDD
Retrocopy KLADFGLSRAFGIPICCY*AGVVTLWYHPPDVFFGAKLYSTSIDLWSAGCIFAELANAGWPLFPGNDVDD

Parental  QLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEA
          QLKRIF.LLG..T.EQWPSMTKLPDYK.YP.YPATTSLVN.VPKLNATGRDLLQNLLKCNP.Q.ISAEEA
Retrocopy QLKRIFWLLGMLTKEQWPSMTKLPDYKLYPLYPATTSLVNIVPKLNATGRDLLQNLLKCNPCQCISAEEA

Parental  LQHPYFSDFCPP
          LQHPYFSDFCPP
Retrocopy LQHPYFSDFCPP

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
SRP007412_brain_prefrontal_cortex	1.43 RPM	51.10 RPM
SRP007412_cerebellum	1.72 RPM	22.62 RPM
SRP007412_heart	0.15 RPM	3.15 RPM
SRP007412_kidney	0.99 RPM	13.63 RPM
SRP007412_liver	0.69 RPM	7.14 RPM
SRP007412_testis	0.00 RPM	1.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2717 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2717 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2717 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4002
Gorilla gorilla	retro_ggor_2686
Pongo abelii	retro_pabe_3290

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
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	ENSPTRG00000005147	1 retrocopy	retro_ptro_180,
Pan troglodytes	ENSPTRG00000019872	1 retrocopy	retro_ptro_2717 ,
Ictidomys tridecemlineatus	ENSSTOG00000016068	1 retrocopy	retro_itri_906,