RetrogeneDB ID: retro_hsap_4783

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:11722643..11723713(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000223418
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LIMK2
• Ensembl ID: ENSG00000182541
• Aliases: None
• Description: LIM domain kinase 2 [Source:HGNC Symbol;Acc:6614]

Sequence

>retro_hsap_4783
GAATGCTTTGCCTGTGTGAGCTATAAGGTGACCATTGAGGATGGGGATGCATACGCCCTGGTGCTGCGTGTCACCCTATA
CTGTGGAAAGTGCCACAAATGAGGTGGTGCTGGCACCCATATTTGAGATACTCTCCACAGAGTCCATTCAGGACCAGCTG
CCCTACTCTGTCATGCTCATGTCCATGCTGGCCATCACAGAGGGCAGGCGGAGCTTCTCCGTGTCCGTGGAGAATGCCTG
CTCCAACTATGTTACCACCGTGCAAGTAAAAGAGGTCAACCAGATGCACATCAGTCCCAACAGCTGCAATGCCATCCACC
CCAGGGACCACATCCTGGAGATCAGTGGAACCCCCACCCACACACTCCAAGTAGAGGAGTTGGAGGATGCAATTAGCCAG
ATGAGCCAGACACTTCTGCTGTTGATTGAACATGACCCTGTCTCCCGGTCCCCAGCCCAGCTGCGGCTGGATGCCTGGCT
CTCTCCCCACACACAGAATGCTGGACACCCTCACGCCCTCAGCACCCTGGACACCAAGGATAATCTGGAGGGGACACTGA
GAAGATGCTCCCTAAGACTCAGTAACAGCATCTCCAAGTCCCCTAGCCCTAGCTCTCCAAAGGAGCCCCTGCTGCTCAGC
CGTGACATCAGCTGCTGGGAATCCCTTTGTTGTTCCAGCACTTACTCAAAGCAGAACTTCCGGTCCTGTGACCTGATCCA
CGGGGAGGTCCTGGGGAAGGGCTTCTTTGGGCAGGCTATCAAAGTGACACACAAAGCCACAGGCAAAGTGTTGGTCATGA
AGGAATTAATGCGATGTGATGAGGAGAACCAGAAGACTTTTCTGACTGAAGTGAAAGTGACGTGAAGCCTGGACCACCCC
AATGTGCTCAAGTTCATTGGCGTGCTGTACAAGGACAAGAAGCTGAACCTGCTGAGAGGACATTGAGGGGGGCATGCTGA
AGGACCTTCTGCAAAGTGTGGACCCATTCCCCTGGCAGCAGGAAGTCAGCTTGGCCAAAGGCATTGCCTCCAGAATGGCC
ACCACCAAGAAATGTACTTTGCACAAGAAC

Alignment

ORF - retro_hsap_4783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.01 %
• Parental protein coverage: 52.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ECFACMSCKVIIEDGDAYALVQHATLYCGKCH-NEVVLAPMFERLSTESVQEQLPYSVTLISMPATTEGR
          ECFAC.S.KV.IEDGDAYALV...TLYCGKCH.NEVVLAP.FE.LSTES.Q.QLPYSV.L.SM.A.TEGR
Retrocopy ECFACVSYKVTIEDGDAYALVLRVTLYCGKCH>NEVVLAPIFEILSTESIQDQLPYSVMLMSMLAITEGR

Parental  RGFSVSVESACSNYATTVQVKEVNRMHISPNNRNAIHPGDRILEINGTPVRTLRVEEVEDAISQTSQTLQ
          R.FSVSVE.ACSNY.TTVQVKEVN.MHISPN..NAIHP.D.ILEI.GTP..TL.VEE.EDAISQ.SQTL.
Retrocopy RSFSVSVENACSNYVTTVQVKEVNQMHISPNSCNAIHPRDHILEISGTPTHTLQVEELEDAISQMSQTLL

Parental  LLIEHDPVSQRLDQLRLEARLAPHMQNAGHPHALSTLDTKENLEGTLRRRSLRRSNSISKSPGPSSPKEP
          LLIEHDPVS....QLRL.A.L.PH.QNAGHPHALSTLDTK.NLEGTLRR.SLR.SNSISKSP.PSSPKEP
Retrocopy LLIEHDPVSRSPAQLRLDAWLSPHTQNAGHPHALSTLDTKDNLEGTLRRCSLRLSNSISKSPSPSSPKEP

Parental  LLFSRDISRSESLRCSSSYSQQIFRPCDLIHGEVLGKGFFGQAIKVTHKATGKVMVMKELIRCDEETQKT
          LL.SRDIS..ESL.CSS.YS.Q.FR.CDLIHGEVLGKGFFGQAIKVTHKATGKV.VMKEL.RCDEE.QKT
Retrocopy LLLSRDISCWESLCCSSTYSKQNFRSCDLIHGEVLGKGFFGQAIKVTHKATGKVLVMKELMRCDEENQKT

Parental  FLTEVKVMRSLDHPNVLKFIGVLYKDKKLNLLTEY-IEGGTLKDFLR-SMDPFPWQQKVRFAKGIASGMA
          FLTEVKV..SLDHPNVLKFIGVLYKDKKLNLL......G.....F...S.DPFPWQQ.V..AKGIAS.MA
Retrocopy FLTEVKVT*SLDHPNVLKFIGVLYKDKKLNLLRGH<LRGAC*RTFCK<SVDPFPWQQEVSLAKGIASRMA

Parental  YLHSMCIIHRD
          .....C..H..
Retrocopy -TTKKCTLHKN

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	36.54 RPM
bodymap2_adrenal	0.00 RPM	81.43 RPM
bodymap2_brain	0.00 RPM	38.96 RPM
bodymap2_breast	0.00 RPM	28.48 RPM
bodymap2_colon	0.00 RPM	26.34 RPM
bodymap2_heart	0.00 RPM	7.51 RPM
bodymap2_kidney	0.00 RPM	39.48 RPM
bodymap2_liver	0.00 RPM	13.82 RPM
bodymap2_lung	0.00 RPM	122.33 RPM
bodymap2_lymph_node	0.00 RPM	65.53 RPM
bodymap2_ovary	0.00 RPM	36.90 RPM
bodymap2_prostate	0.00 RPM	33.13 RPM
bodymap2_skeletal_muscle	0.00 RPM	8.58 RPM
bodymap2_testis	0.00 RPM	28.98 RPM
bodymap2_thyroid	0.00 RPM	90.65 RPM
bodymap2_white_blood_cells	0.00 RPM	61.27 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4783 was not detected

EST

No EST(s) were mapped for retro_hsap_4783 retrocopy.

TSS

No TSS is located nearby retro_hsap_4783 retrocopy 5' end.

Lab

retro_hsap_4783 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4783 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3184
Gorilla gorilla	retro_ggor_2978
Pongo abelii	retro_pabe_3723

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000182541	1 retrocopy	retro_hsap_4783 ,
Gorilla gorilla	ENSGGOG00000003489	1 retrocopy	retro_ggor_2978,
Pongo abelii	ENSPPYG00000011730	1 retrocopy	retro_pabe_3723,
Pan troglodytes	ENSPTRG00000014266	1 retrocopy	retro_ptro_3184,

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	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.05 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	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.02 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	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.04 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	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.00 RPM

---

Indel association:

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