RetrogeneDB ID: retro_hsap_4707

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:73289056..73289892(+)
• Located in intron of: ENSG00000230590

Retrocopy information

• Ensembl ID: ENSG00000234969
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AARSD1
• Ensembl ID: ENSG00000266967
• Aliases: None
• Description: alanyl-tRNA synthetase domain containing 1 [Source:HGNC Symbol;Acc:28417]

Sequence

>retro_hsap_4707
ATGGTGTTCTGGTGTCAGGAGAATAGCAATGCCTGGGAGTCCACCACCACCATAATCTCCTGTGATCCCACGGAGCTGCA
GTCAGAAGGGAGCAATGACAAGAAATAAGTGCTGAGCAGTTGTCATATGGTGCTGGAAGACATGCTACTTTTCCCTGAGG
GCGGAAGACAGCCTGATGACGGTGGTACAATCAATGACATCTCTGTGCTGGGAGTGACCTGCTTGGGGGCCCAGGCTGAT
CATTTCACACAGACACCCCTGGATCCTGGAAGCCAAGTCCTGGTCTGGGTAGACTGGGAGTGGAGGTTTGACCACATGCA
GCAGCATTAAAGGCAGCATCTCATCACAGCAGTTGCTGATTATCTGTTTGAGTTAAAGACAACATCATGGGAGTTAGGGA
AATTTCGGAGTGTGATGCTGGAAAGCCCCTCTGTGAATGCAGAGAAAATAACCGCCACTGAAAAGAGTGTCAATAAAAAT
ATCAGAGATCAGCTGCTCAACAAAGTATGAGAACTGAGCCTGAATGATCCTGAGGCGGAGCAGGTGAGAGGCTGGGGCCT
GCCAGATGATCATGCTGGGCCCATTGGAATTGTTACCATCAAGGGTGTTGATTCCAACATGTGCTGTGGGATCCCCATGA
GCAATCTCCGTGACTTTCCAGTCATTAAGATTAGGCACCGAGAAGAGGAAAAGGAATAAAATCAAACTGATATTTCTGGC
TGGGAACCAGATGCTGAAATGGATGAAGAGAAGTCATGAAACTGAAAGAGCACTGAATCACTCTGCTTAAGTGTGGAGCA
GAGGATCACATGGAAGCAGTGAAAAAGCTCCAGAAT

Alignment

ORF - retro_hsap_4707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.96 %
• Parental protein coverage: 67.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAFWCQRDSYAREFTTTVVSCCPAELQTEGSNGKKEVLSGFQVVLEDTVLFPEGGGQPDDRGTINDISVL
          M.FWCQ..S.A.E.TTT..SC.P.ELQ.EGSN.KK.VLS....VLED..LFPEGG.QPDD.GTINDISVL
Retrocopy MVFWCQENSNAWESTTTIISCDPTELQSEGSNDKK*VLSSCHMVLEDMLLFPEGGRQPDDGGTINDISVL

Parental  RVTRRGEQADHFTQTPLDPGSQVLVRVDWERRFDHMQQHSGQHLITAVADHLFKLKTTSWELGRFRSAIE
          .VT..G.QADHFTQTPLDPGSQVLV.VDWE.RFDHMQQH..QHLITAVAD.LF.LKTTSWELG.FRS...
Retrocopy GVTCLGAQADHFTQTPLDPGSQVLVWVDWEWRFDHMQQH*RQHLITAVADYLFELKTTSWELGKFRS-VM

Parental  LDTPSMTAEQVAAIEQSVNEKIRDRLPVNVRELSLDDPEVEQVSGRGLPDDHAGPIRVVNIEGVDSNMCC
          L..PS..AE...A.E.SVN..IRD.L...V.ELSL.DPE.EQV.G.GLPDDHAGPI..V.I.GVDSNMCC
Retrocopy LESPSVNAEKITATEKSVNKNIRDQLLNKV*ELSLNDPEAEQVRGWGLPDDHAGPIGIVTIKGVDSNMCC

Parental  GTHVSNLSDLQVIKILGTE-KGK-KNRTNLIFLSGNRVLKWMERSHGTEKALT-ALLKCGAEDHVEAVKK
          G...SNL.D..VIKI...E..GK..N...LIFL.GN..LKWM.RSH.TE.AL...LLKCGAEDH.EAVKK
Retrocopy GIPMSNLRDFPVIKIRHRE<RGK<RNKIKLIFLAGNQMLKWMKRSHETERALN>TLLKCGAEDHMEAVKK

Parental  LQN
          LQN
Retrocopy LQN

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	0.52 RPM	1.23 RPM
bodymap2_adrenal	0.88 RPM	9.89 RPM
bodymap2_brain	1.31 RPM	4.36 RPM
bodymap2_breast	0.45 RPM	1.85 RPM
bodymap2_colon	0.19 RPM	1.66 RPM
bodymap2_heart	0.20 RPM	0.44 RPM
bodymap2_kidney	0.39 RPM	2.59 RPM
bodymap2_liver	0.17 RPM	0.59 RPM
bodymap2_lung	0.62 RPM	1.56 RPM
bodymap2_lymph_node	0.00 RPM	4.57 RPM
bodymap2_ovary	0.89 RPM	4.95 RPM
bodymap2_prostate	0.28 RPM	2.75 RPM
bodymap2_skeletal_muscle	0.15 RPM	0.98 RPM
bodymap2_testis	0.15 RPM	3.34 RPM
bodymap2_thyroid	0.66 RPM	3.52 RPM
bodymap2_white_blood_cells	0.18 RPM	0.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4707 was not detected

EST

2 EST(s) were mapped to retro_hsap_4707 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA361102	73289039	73289366	100	322	0	322
BG958680	73289106	73289241	98.4	119	1	109

TSS

No TSS is located nearby retro_hsap_4707 retrocopy 5' end.

Lab

retro_hsap_4707 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4707 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3129

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110958	5 retrocopies	retro_hsap_2084, retro_hsap_3122, retro_hsap_417, retro_hsap_618, retro_hsap_623,
Homo sapiens	ENSG00000266967	1 retrocopy	retro_hsap_4707 ,
Pongo abelii	ENSPPYG00000029909	3 retrocopies	retro_pabe_3654, retro_pabe_3655, retro_pabe_458,
Pan troglodytes	ENSPTRG00000009230	1 retrocopy	retro_ptro_3129,
Ictidomys tridecemlineatus	ENSSTOG00000000481	1 retrocopy	retro_itri_940,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.15 RPM
CEU_NA11843	0.23 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.15 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.44 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.35 RPM
CEU_NA12873	0.16 RPM
FIN_HG00183	0.38 RPM
FIN_HG00277	0.37 RPM
FIN_HG00315	0.33 RPM
FIN_HG00321	0.12 RPM
FIN_HG00328	0.36 RPM
FIN_HG00338	0.21 RPM
FIN_HG00349	0.43 RPM
FIN_HG00375	0.07 RPM
FIN_HG00377	0.25 RPM
FIN_HG00378	0.25 RPM
GBR_HG00099	0.23 RPM
GBR_HG00111	0.21 RPM
GBR_HG00114	0.26 RPM
GBR_HG00119	0.50 RPM
GBR_HG00131	0.26 RPM
GBR_HG00133	0.39 RPM
GBR_HG00134	0.46 RPM
GBR_HG00137	0.30 RPM
GBR_HG00142	0.36 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.17 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.24 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.26 RPM
TSI_NA20765	0.39 RPM
TSI_NA20771	0.57 RPM
TSI_NA20786	0.26 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.37 RPM
YRI_NA18907	0.28 RPM
YRI_NA18916	0.40 RPM
YRI_NA19093	0.23 RPM
YRI_NA19099	0.16 RPM
YRI_NA19114	0.18 RPM
YRI_NA19118	0.35 RPM
YRI_NA19213	0.17 RPM
YRI_NA19214	0.10 RPM
YRI_NA19223	0.24 RPM

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Indel association:

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