RetrogeneDB ID: retro_ggor_2686

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 8:122454310..122455186(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK5
• Ensembl ID: ENSGGOG00000016879
• Aliases: None
• Description: None

Sequence

>retro_ggor_2686
ATGCAGAAATACAAGAAACTGGAGAAGATTGGGGAAGCCACCTATGGGACAGTGTTCAAGGCCAAAAACCGGGAGACTCA
TGAGATTGTGGCTCTGAAATGGGTGAGGCTGGATGACAATGATGAGGGTGTGCCAAGTTCTGCCCTCCGGGAGATCTGCC
TACTCAAGGAGCTGAAGTACAAGAACATCATCAGGCTTCATGACGTCCTGCACAGCGACAAGAAGCTGACTTTGGTTTTC
AAATTCTGTCACCAGCACCTGAAAAAGTATTTTGACAGTTGCAATGGTGACCTCGATTCTGAGATTGTAAAGTCATTCCT
CTTCCAGCTGCTAAAAGGCCTCGGATTCTGTCACAGCCGCAATGTGCTACGCAGGGACCTGAAGCCCCAGAACCTGCTAA
TAAACAGGAATGGGGAGCTGAAATTGGCTGACTTTGGCCTGTATCGAGCCTTTGGGATCCCCATCTGCTGTTACTGAGCT
GGAGTGGTCACACTGTGGTACCACCCACCAGATGTCTTCTTTGGGGCCAAGCTGTACTCCACGTCCATTGACATGTGGTC
AGCTGGCTGCATCTTTGCAGAGCTGGCCAATGCTGGATGGCCTCTTTTTCCAGGCAATGATGTCGATGACCAGTTGAAGA
GGATCTTCCGGCTGCTAGGGATGCTCACCAAGGAGCAGTGGCCCTCCATGACCAAGCTGCCAGACTATAAGCTGTACCCA
ATGTACCCGGCCACAACATCCCTGGTGAACATCGTGCCCAAACTCAATGCCACAGGGAGGGACCTGCTGCAGAATCTTCT
GAAGTGTAACCCCTTCCAATGTATCTCAGCAGAAGAGGCCCTGCAGCACCCCTACTTTTCCGACTTCTGTCCGCCC

Alignment

ORF - retro_ggor_2686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVL
          MQKY.KLEKIGE.TYGTVFKAKNRETHEIVALK.VRLDD.DEGVPSSALREICLLKELK.KNI.RLHDVL
Retrocopy MQKYKKLEKIGEATYGTVFKAKNRETHEIVALKWVRLDDNDEGVPSSALREICLLKELKYKNIIRLHDVL

Parental  HSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDLKPQNLLINRNGEL
          HSDKKLTLVF.FC.Q.LKKYFDSCNGDLD.EIVKSFLFQLLKGLGFCHSRNVL.RDLKPQNLLINRNGEL
Retrocopy HSDKKLTLVFKFCHQHLKKYFDSCNGDLDSEIVKSFLFQLLKGLGFCHSRNVLRRDLKPQNLLINRNGEL

Parental  KLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDD
          KLADFGL.RAFGIP..CY.A.VVTLWY.PPDV.FGAKLYSTSIDMWSAGCIFAELANAG.PLFPGNDVDD
Retrocopy KLADFGLYRAFGIPICCY*AGVVTLWYHPPDVFFGAKLYSTSIDMWSAGCIFAELANAGWPLFPGNDVDD

Parental  QLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEA
          QLKRIFRLLG..T.EQWPSMTKLPDYK.YPMYPATTSLVN.VPKLNATGRDLLQNLLKCNP.Q.ISAEEA
Retrocopy QLKRIFRLLGMLTKEQWPSMTKLPDYKLYPMYPATTSLVNIVPKLNATGRDLLQNLLKCNPFQCISAEEA

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	0.62 RPM	47.57 RPM
SRP007412_cerebellum	0.24 RPM	17.45 RPM
SRP007412_heart	0.09 RPM	3.06 RPM
SRP007412_kidney	0.00 RPM	8.91 RPM
SRP007412_liver	0.03 RPM	6.20 RPM
SRP007412_testis	0.10 RPM	4.45 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2686 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2686 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4002
Pan troglodytes	retro_ptro_2717
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	ENSGGOG00000001404	1 retrocopy	retro_ggor_275,
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,