RetrogeneDB ID: retro_nleu_549

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:36928431..36929307(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000005198
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK5
• Ensembl ID: ENSNLEG00000004100
• Aliases: None
• Description: cyclin-dependent kinase 5 [Source:HGNC Symbol;Acc:1774]

Sequence

>retro_nleu_549
ATGCAGAAATACGAGAAACTGGAGAAGATTGGGGAAGGCACCTACAGGGCAGTGTTCGAGGCCAAAAACCGGGAGACTCA
TGAGATCGTGTCTCTGAAATGGGTGAGGCTGGATGACAACGATGAGGGTGTGCCGAGTTCCGCCCTCCGGGAGATCTGCC
TACTCAAGGAGCTGAAGCACAAGAACAACATCAGGCTTCCTGACGTCCTGCACAGCGACAAGAAGCTGACTTTGGTTTTC
AAATTCTGTCACCAGCACCTGAAAAAGTATTTTGACAGTTGCAATGGTGACCTCGATCCTGAGATTGTAAAGTCATTCCT
CTTCCAGCTGCTAAAAGGCCTGGCATTCTGTCACAGCCGCAATGTGCTACGCAGGGACCTGAAGCCCCAGAACCTGCTAA
TAAACAGGAATGGGGAGCTGAAATTGGCTGACTTTGGCCTGTCTCGAGCCTTTGGGATCCCCATCTGCTGTTACTGAGCT
GGAGTGCTCACACTGTGGTACCGCCCACCAGATGTCTTCTTTGGGGCCAAGCTGTACTCCACATCCATTGACATGTGGTC
AGCTGGCTGCATCTTTGCAGAGCTGGCCAATGTTAGACGGCCTCTTTTTCCAGGCAATGATGTCGATGACCAGTTGAAGA
GGATCTTCCGGCTGCGAGGGACGCCCACCAAGGAACAGTGGCCCTCCATGACCAAGCTGCCAGACTATAAGCCGTACCCA
ATGTACCCGGCCACAACATTCCTGGTGAACGTCGTGCCCAAACTCAATGCCACAGGGAGGGACCTGCTGCAGAATCTTCT
GAAGTGTAACCCCATCCAGTGTATCTCAGCAGAAGAGGCCCTGCAGCACCCCTACTTTTCTGACTTCTGTCCGCCC

Alignment

ORF - retro_nleu_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVL
          MQKYEKLEKIGEGTY..VF.AKNRETHEIV.LK.VRLDD.DEGVPSSALREICLLKELKHKN..RL.DVL
Retrocopy MQKYEKLEKIGEGTYRAVFEAKNRETHEIVSLKWVRLDDNDEGVPSSALREICLLKELKHKNNIRLPDVL

Parental  HSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDLKPQNLLINRNGEL
          HSDKKLTLVF.FC.Q.LKKYFDSCNGDLDPEIVKSFLFQLLKGL.FCHSRNVL.RDLKPQNLLINRNGEL
Retrocopy HSDKKLTLVFKFCHQHLKKYFDSCNGDLDPEIVKSFLFQLLKGLAFCHSRNVLRRDLKPQNLLINRNGEL

Parental  KLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDD
          KLADFGL.RAFGIP..CY.A.V.TLWYRPPDV.FGAKLYSTSIDMWSAGCIFAELAN..RPLFPGNDVDD
Retrocopy KLADFGLSRAFGIPICCY*AGVLTLWYRPPDVFFGAKLYSTSIDMWSAGCIFAELANVRRPLFPGNDVDD

Parental  QLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEA
          QLKRIFRL.GTPT.EQWPSMTKLPDYKPYPMYPATT.LVNVVPKLNATGRDLLQNLLKCNP.Q.ISAEEA
Retrocopy QLKRIFRLRGTPTKEQWPSMTKLPDYKPYPMYPATTFLVNVVPKLNATGRDLLQNLLKCNPIQCISAEEA

Parental  LQHPYFSDFCPP
          LQHPYFSDFCPP
Retrocopy LQHPYFSDFCPP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_549 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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 ,
Nomascus leucogenys	ENSNLEG00000017205	1 retrocopy	retro_nleu_1847,
Pongo abelii	ENSPPYG00000018183	1 retrocopy	retro_pabe_3290,
Pan troglodytes	ENSPTRG00000019872	1 retrocopy	retro_ptro_2717,
Ictidomys tridecemlineatus	ENSSTOG00000016068	1 retrocopy	retro_itri_906,