RetrogeneDB ID: retro_pabe_3290

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:130504999..130505875(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK5
• Ensembl ID: ENSPPYG00000018183
• Aliases: None
• Description: cyclin-dependent kinase 5 [Source:HGNC Symbol;Acc:1774]

Sequence

>retro_pabe_3290
ATGCAGAAATACGAGAAACTGGAGAAGATTGGGGAAGGCACCTACAGGACAGTGTTCAAGGCCAAAAACTGGGAGACTCA
TGAGATCGTGGCTCTGAAATGGGTGAGGCTGGATGACAATGATGAGGGTGTGCCGAGTTCCGCCCTCCGGGAGGTCTGCC
TACTCAAGGAGCTGAAGCACAAGAACATCGTCAGGCTTCATGACGTCCTGCACAGCGACAAGAAGCTGACTTTGGTTTTC
AAACTCTGTCAACAGCACCTGAAAAAGTATTTTGACAGTTGCAATGGTGACCTTGATCCTGAGATTGTAAAGTCACTCCT
CTTCCAGCTGCTAAAAGGCCTGGGATTCTGTCACAGCAGCAATGTGCTACGCAGGGACCTGAAGCCCCAGAACCTGCTAA
TAAACAGGAACGAGGAGCTGAAATTGGCTGACTGTGGCCTGTCTCGAGCTTTTTGGATCCCCATCTGCTGTTACTGAGCT
GGAGTGGTCACACTGTGGTACCGCCCACCAGATGTCTTCTTTGGGGCCAAGCCGTACTCCACATCCATTGACATGTGGTC
AGCCGGCTGCATCTTTGCAGAGCTGGCCAATGCTGGACAGCCTCTTTTTCCAGGCAATGATGTCAACGACCAGTTGAAGA
GGATTTTCCAGCTGCTAGGGACGCCCACCGAGGAGCAGTGGCCCTCCATGACCAAACTGCCAGACTATAAGCTGTACCCA
ATGTACCTGGCCACAACATCCCTGGTGAACGTCGTGCCTAAACTCAATGCCACAGGAAGGGACCTGCTGCAGAATCTTCT
GAAGTGTAACCCCGTCCAAAGTATCTCAGCAGAAGAGGCCCTGCAGCAACCCTACTTCTCTGACTTCTGTCCACCC

Alignment

ORF - retro_pabe_3290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVL
          MQKYEKLEKIGEGTY.TVFKAKN.ETHEIVALK.VRLDD.DEGVPSSALRE.CLLKELKHKNIVRLHDVL
Retrocopy MQKYEKLEKIGEGTYRTVFKAKNWETHEIVALKWVRLDDNDEGVPSSALREVCLLKELKHKNIVRLHDVL

Parental  HSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDLKPQNLLINRNGEL
          HSDKKLTLVF..C.Q.LKKYFDSCNGDLDPEIVKS.LFQLLKGLGFCHS.NVL.RDLKPQNLLINRN.EL
Retrocopy HSDKKLTLVFKLCQQHLKKYFDSCNGDLDPEIVKSLLFQLLKGLGFCHSSNVLRRDLKPQNLLINRNEEL

Parental  KLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDD
          KLAD.GL.RAF.IP..CY.A.VVTLWYRPPDV.FGAK.YSTSIDMWSAGCIFAELANAG.PLFPGNDV.D
Retrocopy KLADCGLSRAFWIPICCY*AGVVTLWYRPPDVFFGAKPYSTSIDMWSAGCIFAELANAGQPLFPGNDVND

Parental  QLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEA
          QLKRIF.LLGTPTEEQWPSMTKLPDYK.YPMY.ATTSLVNVVPKLNATGRDLLQNLLKCNPVQ.ISAEEA
Retrocopy QLKRIFQLLGTPTEEQWPSMTKLPDYKLYPMYLATTSLVNVVPKLNATGRDLLQNLLKCNPVQSISAEEA

Parental  LQHPYFSDFCPP
          LQ.PYFSDFCPP
Retrocopy LQQPYFSDFCPP

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	0.06 RPM	48.66 RPM
SRP007412_cerebellum	0.00 RPM	16.54 RPM
SRP007412_heart	0.00 RPM	1.38 RPM
SRP007412_kidney	0.03 RPM	8.29 RPM
SRP007412_liver	0.00 RPM	4.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3290 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3290 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4002
Pan troglodytes	retro_ptro_2717
Gorilla gorilla	retro_ggor_2686

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 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	ENSPTRG00000019872	1 retrocopy	retro_ptro_2717,
Ictidomys tridecemlineatus	ENSSTOG00000016068	1 retrocopy	retro_itri_906,