RetrogeneDB ID: retro_hsap_4690

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:63652280..63654026(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000230889
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SHC1
• Ensembl ID: ENSG00000160691
• Aliases: SHC1, SHC, SHCA
• Description: SHC (Src homology 2 domain containing) transforming protein 1 [Source:HGNC Symbol;Acc:10840]

Sequence

>retro_hsap_4690
ATGAATCTCCTGCCCCCCAAGTCCAAGTGCAATCCACTGTGGAATGAGTCTCTGTCATCGCTGGAGGAGGGGCCTTCAGG
GTCCACCCCACCAGAGGAGCTGCCTTCCCCATCAGCCTCATCCCTGGGGCCCATCCTGCCCCCTCTGCCTGGGAACCATA
GTCCCACTACCCTGTGCTCCTTCTTCCCCTGGATGAGCAACCTGAGGCTGGCCAATTGGGCCGGGGGACACCTGGGGCCT
AATGGGGAGCCAGGAAGGGCAGCCAATGATGGGGAGGGCATTGTAGGGGCAACCATGCCAGACTCATTCCCCTACCCCTC
CTCCAGGACATGAACAAGCTGAGTGGAGGTGGTGGGTGCAGGACTCAGGTGGAAGGGGGCCAGCTGGGGGGTGAGGAGTG
GACCCGCCATGGGAGCTTTGTCAATAAGCCCATGTGGGGCTAGCTGCATCCCAATGACAAAGTCACGAGACCTGGGGTTT
CCTACTTGGTTTGGTACATGGGCTGTGTGGAGGTCCTGCAGTCAATGAGTGCCCTGGACTTCAACACCTGGACTCAGGTC
ACCAGGGAGGCCATCAGTTTTGTGTGTGAGGCTGTGCCAGGTGCCAAGGGGGTGACAAGGAGGAGAAAGCCCTGTAACCA
TCCACTCAGCTCTATCTTGGGAAGGAGTAACCTGAAATTTGCTGCAATGACAATCACTCTCACCATCTCCACCAGCAGCC
TCAACGTCATGGTTGCAGACTGCAAACAGATTATCACTAACCACCATATGCAATCTATCTCACTTGCATCCAGTGGGGAT
CCGGACACAGCCAAGTATGTCGCCAACGTTGCCAAAGACCCTGTGAGTCAGAAAGCATGCCACATTCTGGAGTGTCCTGA
AGGGCTTGCTCAGGATGTCATCAGCACCACTGGCCAGGCCTTCAAGTTGCACTTTAAACAATACCTCAGAAAACCACCCA
AACTGGTCACCCCCCATGACAGGATGACTGGCTTTGATGGCTTAGCTTGGGATGAGGAGGAGGAAGAGCCGCCTGGCCAT
CAGCACTATAATGACTTCCTGGGAAGGAATCCCCTCTTTGGCATGTGGTATACATGAGGCTTCGGGAAGGAGCCACTCCA
GGGGCTGCTCGACCCACTCCACCCAGTGCCCAGACCCCCAGCCACTTGGGATCTACACTGCCTGTAGGACAGTCTGTTGG
GGGAGATCCAGAAGTTTGCAAATAGATGCCACCTCCACCACCCTGTCCAGGCAGAGAGCTCTTTGATGATCCCTCCAATG
TCAACGTGCAGAACCTAGACAAGGCCCGGCAAGCAGGGGGTGGTGCTGGGACCCCCAATCCTGCCATCAATGGCAGCACA
CCCTGAGACCTGTTTGACATGAAGCCCTTTGAAGACACTCTTCACATGCCTCCTCTTCCCCAGTTGGTGTCCATGGCTAA
GCAGCTCTGAGGGGACCCTGGTTCCAAGGGAAGCTGAGCTAGCAGGGGGCTGAGGCACTGCTGCAGTTCAATGGGGACTT
CCTGGTGCAGGAGAGCATGACCACACCTGGCCAGTATGTGCTCACTGGCTTGCAGAGTGGGGAGTCCAAGCATCTGCTAC
TGGTGGACCCTGAGGGTGTAGTTCGGACAAAGGATCACCGCTTTGAGAGTGTCAGTCACCTCATCAGCTACCACATGGAC
AATCACTTGCCCATCACCTCTGCTGGCAGTGAATTGTGTCTACAGCAACCTGTGGAGCAGAAACTG

Alignment

ORF - retro_hsap_4690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.98 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDLLPPKPKYNPLRNESLSSLEEGASGSTPPEELPSPSASSLGPILPPLPGDDSPTTLCSFFPRMSNLRL
          M.LLPPK.K.NPL.NESLSSLEEG.SGSTPPEELPSPSASSLGPILPPLPG..SPTTLCSFFP.MSNLRL
Retrocopy MNLLPPKSKCNPLWNESLSSLEEGPSGSTPPEELPSPSASSLGPILPPLPGNHSPTTLCSFFPWMSNLRL

Parental  ANPAGGRPGSKGEPGRAADDGEGIVGAAMPDSGP-LPLLQDMNKLSGGGGRRTRVEGGQLGGEEWTRHGS
          AN.AGG..G..GEPGRAA.DGEGIVGA.MPDS.P.LPLLQDMNKLSGGGG.RT.VEGGQLGGEEWTRHGS
Retrocopy ANWAGGHLGPNGEPGRAANDGEGIVGATMPDSFP<LPLLQDMNKLSGGGGCRTQVEGGQLGGEEWTRHGS

Parental  FVNKPTRGWLHPNDKVMGPGVSYLVRYMGCVEVLQSMRALDFNTRTQVTREAISLVCEAVPGAKGATRRR
          FVNKP..G.LHPNDKV..PGVSYLV.YMGCVEVLQSM.ALDFNT.TQVTREAIS.VCEAVPGAKG.TRRR
Retrocopy FVNKPMWG*LHPNDKVTRPGVSYLVWYMGCVEVLQSMSALDFNTWTQVTREAISFVCEAVPGAKGVTRRR

Parental  KPCSRPLSSILGRSNLKFAGMPITLTVSTSSLNLMAADCKQIIANHHMQSISFASGGDPDTAEYVAYVAK
          KPC..PLSSILGRSNLKFA.M.ITLT.STSSLN.M.ADCKQII.NHHMQSIS.AS.GDPDTA.YVA.VAK
Retrocopy KPCNHPLSSILGRSNLKFAAMTITLTISTSSLNVMVADCKQIITNHHMQSISLASSGDPDTAKYVANVAK

Parental  DPVNQRACHILECPEGLAQDVISTIGQAFELRFKQYLRNPPKLVTPHDRMAGFDGSAWDEEEEEPPDHQY
          DPV.Q.ACHILECPEGLAQDVIST.GQAF.L.FKQYLR.PPKLVTPHDRM.GFDG.AWDEEEEEPP.HQ.
Retrocopy DPVSQKACHILECPEGLAQDVISTTGQAFKLHFKQYLRKPPKLVTPHDRMTGFDGLAWDEEEEEPPGHQH

Parental  YNDF-PGKEPPLGGVVDMRLREGAAPGAARPTAPNAQTPSHLGATLPVGQPVGGDPEVRKQMPPPPPCPG
          YNDF.PGKE.PL..VV.MRLREGA.PGAARPT.P.AQTPSHLG.TLPVGQ.VGGDPEV.K.MPPPPPCPG
Retrocopy YNDF<PGKESPLWHVVYMRLREGATPGAARPTPPSAQTPSHLGSTLPVGQSVGGDPEVCK*MPPPPPCPG

Parental  RELFDDPSYVNVQNLDKARQAVGGAGPPNPAINGSAPRDLFDMKPFEDALRVPPPPQSVSMAEQLRGE-P
          RELFDDPS.VNVQNLDKARQA.GGAG.PNPAINGS.P.DLFDMKPFED.L..PP.PQ.VSMA.QL.G..P
Retrocopy RELFDDPSNVNVQNLDKARQAGGGAGTPNPAINGSTP*DLFDMKPFEDTLHMPPLPQLVSMAKQL*GD<P

Parental  WFHGKLSRREAEALLQLNGDFLVRESTTTPGQYVLTGLQSGQPKHLLLVDPEGVVRTKDHRFESVSHLIS
          WF.GKLS...AEALLQ.NGDFLV.ES.TTPGQYVLTGLQSG..KHLLLVDPEGVVRTKDHRFESVSHLIS
Retrocopy WFQGKLS*QGAEALLQFNGDFLVQESMTTPGQYVLTGLQSGESKHLLLVDPEGVVRTKDHRFESVSHLIS

Parental  YHMDNHLPIISAGSELCLQQPVERKL
          YHMDNHLPI.SAGSELCLQQPVE.KL
Retrocopy YHMDNHLPITSAGSELCLQQPVEQKL

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	187.55 RPM
bodymap2_adrenal	0.00 RPM	217.06 RPM
bodymap2_brain	0.00 RPM	19.85 RPM
bodymap2_breast	0.04 RPM	88.64 RPM
bodymap2_colon	0.00 RPM	110.99 RPM
bodymap2_heart	0.00 RPM	29.37 RPM
bodymap2_kidney	0.00 RPM	68.37 RPM
bodymap2_liver	0.00 RPM	65.19 RPM
bodymap2_lung	0.00 RPM	131.65 RPM
bodymap2_lymph_node	0.00 RPM	123.60 RPM
bodymap2_ovary	0.00 RPM	91.97 RPM
bodymap2_prostate	0.00 RPM	75.08 RPM
bodymap2_skeletal_muscle	0.00 RPM	34.16 RPM
bodymap2_testis	0.00 RPM	52.58 RPM
bodymap2_thyroid	0.02 RPM	90.67 RPM
bodymap2_white_blood_cells	0.00 RPM	58.41 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4690 was not detected

EST

No EST(s) were mapped for retro_hsap_4690 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_200650	1260 libraries	298 libraries	265 libraries	5 libraries	1 library
TSS #2	TSS_200651	1489 libraries	239 libraries	96 libraries	5 libraries	0 libraries

The graphical summary, for retro_hsap_4690 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_4690 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4690 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3117
Pongo abelii	retro_pabe_3643

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009236	1 retrocopy	retro_cjac_2573,
Homo sapiens	ENSG00000160691	1 retrocopy	retro_hsap_4690 ,
Nomascus leucogenys	ENSNLEG00000011515	1 retrocopy	retro_nleu_2362,
Pongo abelii	ENSPPYG00000000769	1 retrocopy	retro_pabe_3643,
Pan troglodytes	ENSPTRG00000001397	1 retrocopy	retro_ptro_3117,
Tarsius syrichta	ENSTSYG00000011380	1 retrocopy	retro_tsyr_1773,