RetrogeneDB ID: retro_hsap_4002

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:123781512..123782388(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000235165
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDK5
• Ensembl ID: ENSG00000164885
• Aliases: None
• Description: cyclin-dependent kinase 5 [Source:HGNC Symbol;Acc:1774]

Sequence

>retro_hsap_4002
ATGCAGAAATAAAAGAAACTGGAGAAGATTGGGGAAGGCACCTATGGGACAGTGTTCAAGGCCAAAAACTGGGAGACTCA
TGAGATTGTGGCTCTGAAATGGGTGAGGCTGGATGACAATGATGACGGTGTGCCGAGTTCTGCCCTCCGGGAGATCTGCC
TACTCAAGGAGCTGAAGCACAAGAACATCGTCAGGCTTCATGACCTCCTGCACAGCGACAAGAAGCTGACTTTGGTTTTC
AAATTCTGTCACCAGCACCTGAAAAAGTATTTTGACAGTTGCAATGGTGATCTCGATCCTGAGATTGTAAAGTCATTTCT
CTTCCAGCTGCTAAAAGGCCTCGGATTCTGTCACAGCCGCAATGTGCTACGCAGGGACCTGAAGCCCCAGAACCTGCTAA
TAAACAGGAATGGGGAGCTGAAATTGGCTGACTTTGGCCTGTCTCGAGCCTTTGGGATCCCCATCTGCTGTTACTGAGCT
GGAGTGGTCACACTGTGGTACCACCCACCAGATGTCTTCTTTGGGGCCAAGCTGTACTCCACGTCCATTGACTTGTGGTC
AGCTGGCTGCATCTTTGCAGAGCTGGCCAATGCTGGATGGCCTCTTTTTCCAGGCAATGACGTCGATGACCAGTTGAAGA
GGATCTTCTGGCTGCTAGGGATGCTCACCAAGGAGCAGTGGCCCTCCATGACCAAGCTGCCAGACTATAAGCTGTACCCA
TTGTACCCGGCCACAACATCCCTGGTGAACATCGTGCCCAAACTCAGTGCCACAGGGAGGGATCTGCTGCAGAATCTTCT
GAAGTGTAACCCCTGCCAATGTATCTCAGCAGAAGAGGCCCTGCAGTACCCCTACTTTTCCGACTTCTGTCCGCCC

Alignment

ORF - retro_hsap_4002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.38 %
• 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.D.GVPSSALREICLLKELKHKNIVRLHD.L
Retrocopy MQK*KKLEKIGEGTYGTVFKAKNWETHEIVALKWVRLDDNDDGVPSSALREICLLKELKHKNIVRLHDLL

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.VPKL.ATGRDLLQNLLKCNP.Q.ISAEEA
Retrocopy QLKRIFWLLGMLTKEQWPSMTKLPDYKLYPLYPATTSLVNIVPKLSATGRDLLQNLLKCNPCQCISAEEA

Parental  LQHPYFSDFCPP
          LQ.PYFSDFCPP
Retrocopy LQYPYFSDFCPP

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
bodymap2_adipose	0.00 RPM	2.33 RPM
bodymap2_adrenal	0.00 RPM	4.32 RPM
bodymap2_brain	0.00 RPM	26.11 RPM
bodymap2_breast	0.00 RPM	4.61 RPM
bodymap2_colon	0.00 RPM	3.79 RPM
bodymap2_heart	0.00 RPM	2.84 RPM
bodymap2_kidney	0.00 RPM	6.66 RPM
bodymap2_liver	0.00 RPM	5.11 RPM
bodymap2_lung	0.00 RPM	1.64 RPM
bodymap2_lymph_node	0.00 RPM	6.91 RPM
bodymap2_ovary	0.00 RPM	2.97 RPM
bodymap2_prostate	0.00 RPM	4.59 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.07 RPM
bodymap2_testis	0.00 RPM	6.67 RPM
bodymap2_thyroid	0.00 RPM	4.11 RPM
bodymap2_white_blood_cells	0.00 RPM	8.17 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4002 was not detected

EST

No EST(s) were mapped for retro_hsap_4002 retrocopy.

TSS

No TSS is located nearby retro_hsap_4002 retrocopy 5' end.

Lab

retro_hsap_4002 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4002 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2717
Gorilla gorilla	retro_ggor_2686
Pongo abelii	retro_pabe_3290

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.03 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).