RetrogeneDB ID: retro_hsap_3785

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:128766571..128767768(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000230626
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAP2K2
• Ensembl ID: ENSG00000126934
• Aliases: MAP2K2, CFC4, MAPKK2, MEK2, MKK2, PRKMK2
• Description: mitogen-activated protein kinase kinase 2 [Source:HGNC Symbol;Acc:6842]

Sequence

>retro_hsap_3785
ATGCTGGCCCGGAGGAAGCCGATGCTGCCGGCGCTCACCATCAACCCTACCATCGCCGAGGGCCCGTCCCCAACCAGCGA
GGGCGCCTCCGAGGCAAACCTGGTGGACCTGCAGAAGAAGCTGGAGGAGCTGGAACTTGACGAGCAGCAGAAGCGGCTGG
AAGCCTTTCTCACCCAGAAAGCCAAGGTCGGCGAACTCAAAGACGATGACTTCGAAAGGACCTCAGAGCTGGACGCGGGC
AACGGCGGGGTGGTCACCAAAGTCCAGCACAGACCCTCGGGCCTCATCATGGCCAGGAAGCTGATCCACCTTGAGATCAA
GCCGGCCATCCGGAACCAGATCATCCGCGAGCACCAGGTCCTGCACGAGTGCAACTCACCGTACATCGTGGGCTTCTACG
GGGCCTTCTACTGTGACAGGGAGATCAGCATCTGCATGGAGCACATGGATGGCGGCTCCCTGGACCAGGGGCTGAAAGAG
GCCAAGAGGATTCCCGAGGACATCCTGGGGAAAGTCAGCATTGCGGTTCTCCGGGGCTTGGCGTACCTCCGAGAGAAGCA
CCAGATCATGCACCGAAATGTGAAGCCCTCCAACATCCTCGTGAACTCTAGAGGGGAGATCAAGCTGTGTGACTTCGGGG
TGAGCGGCCAGCTCATCGACTCCATGGCCAACTCCTTCGTGGGCACGCGCTCCTACATGGCTCCGGAGCGGTTGCAGGGC
ACACATTACTCGGTGCAGTCGGTCATCTGGAGCATGGACCTGTCCCTGGTGGAGCTGGCCATCGAAAGGTACCCCATCCC
CCCGCCCGACGCCAAGGAGCTGGAGGCCATCTTTGGCCAGCCCGTGGTCGACAGGGAAGAAGGAGAGCCTCACAGCATCT
CCTCTTGGCCAGGGTCCCCCGGGCGCCCCAACAGCGGTTACGGGATGGACAGCCTGCCCGCCATGGCCATCTTCGAACTG
CTGGACTATATTGTGAAAGAGCCGCCTCCTAAGCTGCCCAACGGTGTGTTCACCCCCGACTTCCAGGAGTTTGTCAATAA
ATGCCTCATCAAAAACCCAACGGAGCGGGCGGACCTAAAGATGCTCACAAACCACGCCTTCATCAAGCGGTCCGAGGTGA
AAGAAGCGGATTTTGCCTGCTAGTTGTGTAAAACCCTGGGGCTGAACCAGCCCGGCACACCCACGCGCACCGCCGTG

Alignment

ORF - retro_hsap_3785 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLARRKPVLPALTINPTIAEGPSPTSEGASEANLVDLQKKLEELELDEQQKKRLEAFLTQKAKVGELKDD
          MLARRKP.LPALTINPTIAEGPSPTSEGASEANLVDLQKKLEELELDEQQK.RLEAFLTQKAKVGELKDD
Retrocopy MLARRKPMLPALTINPTIAEGPSPTSEGASEANLVDLQKKLEELELDEQQK-RLEAFLTQKAKVGELKDD

Parental  DFERISELGAGNGGVVTKVQHRPSGLIMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSD
          DFER.SEL.AGNGGVVTKVQHRPSGLIMARKLIHLEIKPAIRNQIIRE.QVLHECNSPYIVGFYGAFY.D
Retrocopy DFERTSELDAGNGGVVTKVQHRPSGLIMARKLIHLEIKPAIRNQIIREHQVLHECNSPYIVGFYGAFYCD

Parental  GEISICMEHMDGGSLDQVLKEAKRIPEEILGKVSIAVLRGLAYLREKHQIMHRDVKPSNILVNSRGEIKL
          .EISICMEHMDGGSLDQ.LKEAKRIPE.ILGKVSIAVLRGLAYLREKHQIMHR.VKPSNILVNSRGEIKL
Retrocopy REISICMEHMDGGSLDQGLKEAKRIPEDILGKVSIAVLRGLAYLREKHQIMHRNVKPSNILVNSRGEIKL

Parental  CDFGVSGQLIDSMANSFVGTRSYMAPERLQGTHYSVQSDIWSMGLSLVELAVGRYPIPPPDAKELEAIFG
          CDFGVSGQLIDSMANSFVGTRSYMAPERLQGTHYSVQS.IWSM.LSLVELA..RYPIPPPDAKELEAIFG
Retrocopy CDFGVSGQLIDSMANSFVGTRSYMAPERLQGTHYSVQSVIWSMDLSLVELAIERYPIPPPDAKELEAIFG

Parental  RPVVDGEEGEPHSISPRPRPPGRPVSGHGMDSRPAMAIFELLDYIVNEPPPKLPNGVFTPDFQEFVNKCL
          .PVVD.EEGEPHSIS..P..PGRP.SG.GMDS.PAMAIFELLDYIV.EPPPKLPNGVFTPDFQEFVNKCL
Retrocopy QPVVDREEGEPHSISSWPGSPGRPNSGYGMDSLPAMAIFELLDYIVKEPPPKLPNGVFTPDFQEFVNKCL

Parental  IKNPAERADLKMLTNHTFIKRSEVEEVDFAGWLCKTLRLNQPGTPTRTAV
          IKNP.ERADLKMLTNH.FIKRSEV.E.DFA..LCKTL.LNQPGTPTRTAV
Retrocopy IKNPTERADLKMLTNHAFIKRSEVKEADFAC*LCKTLGLNQPGTPTRTAV

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	0.04 RPM	51.36 RPM
bodymap2_adrenal	0.06 RPM	52.57 RPM
bodymap2_brain	0.33 RPM	30.96 RPM
bodymap2_breast	0.02 RPM	44.69 RPM
bodymap2_colon	0.23 RPM	50.51 RPM
bodymap2_heart	0.00 RPM	32.93 RPM
bodymap2_kidney	0.00 RPM	36.48 RPM
bodymap2_liver	0.00 RPM	35.02 RPM
bodymap2_lung	0.02 RPM	33.81 RPM
bodymap2_lymph_node	0.09 RPM	56.05 RPM
bodymap2_ovary	0.02 RPM	51.18 RPM
bodymap2_prostate	0.03 RPM	41.31 RPM
bodymap2_skeletal_muscle	0.00 RPM	71.28 RPM
bodymap2_testis	1.36 RPM	78.75 RPM
bodymap2_thyroid	0.04 RPM	50.62 RPM
bodymap2_white_blood_cells	0.14 RPM	52.96 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3785 was not detected

EST

3 EST(s) were mapped to retro_hsap_3785 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DB021225	128766537	128767058	99.3	520	1	518
HY016988	128766533	128767090	99.7	554	2	552
HY038562	128766549	128767002	98.9	448	5	443

TSS

No TSS is located nearby retro_hsap_3785 retrocopy 5' end.

Lab

retro_hsap_3785 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3785 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2566
Gorilla gorilla	retro_ggor_115

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015084	1 retrocopy	retro_cjac_4061,
Equus caballus	ENSECAG00000009157	2 retrocopies	retro_ecab_668, retro_ecab_968,
Homo sapiens	ENSG00000065559	1 retrocopy	retro_hsap_4858,
Homo sapiens	ENSG00000126934	1 retrocopy	retro_hsap_3785 ,
Gorilla gorilla	ENSGGOG00000008832	1 retrocopy	retro_ggor_115,
Nomascus leucogenys	ENSNLEG00000003013	1 retrocopy	retro_nleu_1121,
Otolemur garnettii	ENSOGAG00000001658	1 retrocopy	retro_ogar_576,
Pan troglodytes	ENSPTRG00000010294	1 retrocopy	retro_ptro_2566,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.13 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.06 RPM
FIN_HG00183	0.14 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.04 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.07 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.06 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.13 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.07 RPM
YRI_NA19214	0.02 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).