RetrogeneDB ID: retro_hsap_4254

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:38487318..38488173(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000229511
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GAS2L1
• Ensembl ID: ENSG00000185340
• Aliases: GAS2L1, GAR22
• Description: growth arrest-specific 2 like 1 [Source:HGNC Symbol;Acc:16955]

Sequence

>retro_hsap_4254
TCTGCACCCGGTCAGCTCCCCAAGATAAAGGCCTCGGAGGGGAAGTTCCGCGTGGGAGACTCCGGCCTGTTGATCTCTGT
GAGGGTGCCCGGGAGCCGCCTGACGGCGCGCCTGGGTGTGGCGACCCGCTGGAGCGCTACCTGGACAGTCAGGACCCGCG
CCGCCGCTCCTCCACCACCCACCGCCCGCCCCCGTCGAGGGTCCGCACCCTGTCCCCGCAGAGGGTGTCGCCCACCCCTA
GCCCCTGCCCTGGTAGCCTGGTCCCCGCGAGAGAGCGCCGGCGCTCCGGACCCTAGGTGACCCCTATTCGCTTACAAAGC
ATAAAGCAGGGGCCGAGGCTCCCAGGCCCTGGGATCAGCTGCCCGCCGCATCCCCGCTCCTACTCTGAGGACAGTGACTC
CTCAGCTTTCTCAGCCCAGAGCCGCCCCCTTGGTGCCCGCAGCGAGGATGAGGCACTAGGCCGGGAGGAAGAGACCCAGA
CGGGGGCTGACCACCACCACCTGGCCTCTCCGAGACGGCCCCCTGCCCCGCGCAGCCAGTCCCGGGACGGGCTGGATCCG
AGTCGGCCCCGGGGAGCTCCAGGAGAGAGGGGAGCCCAGCTGCGGCCCTCAGCCCTGCCCGGTGGGCGCAGGAGCAGACT
GGGCTCAAGGATGGAGATGGGCAGCACTCGTGGGAGCCACAGGGCAGGGGCAGCGGGGCTCGGGCAGGAGCACCCCTGGG
CTCTCCATGCCCACCGCCCTGAAGCACCCTGGCTTTCCCAGTCCAACCCCAGTTTAGAGTTTAGCACCACACGCGCCAGC
GTCTTCCGCACACACCAGAGCAGCTGCTCTGACGCCTGGACAAGGAGTTTCTGGC

Alignment

ORF - retro_hsap_4254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.84 %
• Parental protein coverage: 55.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  TCPDQFPMIKVSEGKYRVGDSSLLIFVRVLRSHVMVRV-GGGWDTLEHYLDKHDPCRCSSTAHRPPQPRV
          ..P.Q.P.IK.SEGK.RVGDS.LLI.VRV..S....R..G.G.D.LE.YLD..DP.R.SST.HRPP..RV
Retrocopy SAPGQLPKIKASEGKFRVGDSGLLISVRVPGSRLTARL<GCG-DPLERYLDSQDPRRRSSTTHRPPPSRV

Parental  CTFSPQRVSPTTSPRPASPVPGSERRGSRPEMTPVSLRSTKE-GPETPPRPRDQLP-PHPRSRRYSGDSD
          .T.SPQRVSPT.SP.P.S.VP..ERR.S.P..TP..L.S.K..G.E.P.RP.DQLP.PHPRS..YS.DSD
Retrocopy RTLSPQRVSPTPSPCPGSLVPARERRRSGP*VTPIRLQSIKQ<GAEAP-RPWDQLP>PHPRS--YSEDSD

Parental  SSASSAQSGPLGTRSDDT-GTGPR-RERPSRRLTTGT-PASPRRPPACAASPETGWIAAGPGGPQEAGEP
          SSA.SAQS.PLG.RS.D..GT.P..R.RP.R.LTT.T..ASPRRPPA.......G.....P.G.......
Retrocopy SSAFSAQSRPLGARSEDE<GTRPG<RKRPRRGLTTTT<LASPRRPPAPRSQSRDGLDPSRPRGAPGERGA

Parental  SCRSPALPGGPGARAARSRLCCLCAGIETGSTHGCQGAGAVG-ARAGAP-PRLPVPAALQHPGFPGSPAP
          ..R..AL...PG.R..RSR...L....E.GST.G...AGA.G.ARAGAP.P.L..P.AL.HPGFP.SP.P
Retrocopy QLRPSAL---PGGR--RSR---LGSRMEMGSTRGSHRAGAAG<ARAGAP<PGLSMPTALKHPGFP-SPTP

Parental  VQSWAPHRPASSAHPCSSTRSRSSSCSG
          V.S.APH.PASSAH............SG
Retrocopy V*SLAPHAPASSAHTRAAALTPGQGVSG

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	9.60 RPM
bodymap2_adrenal	0.00 RPM	10.23 RPM
bodymap2_brain	0.00 RPM	10.34 RPM
bodymap2_breast	0.00 RPM	26.07 RPM
bodymap2_colon	0.00 RPM	10.52 RPM
bodymap2_heart	0.00 RPM	7.86 RPM
bodymap2_kidney	0.00 RPM	13.07 RPM
bodymap2_liver	0.00 RPM	7.16 RPM
bodymap2_lung	0.00 RPM	6.35 RPM
bodymap2_lymph_node	0.00 RPM	8.64 RPM
bodymap2_ovary	0.00 RPM	8.08 RPM
bodymap2_prostate	0.00 RPM	10.96 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.36 RPM
bodymap2_testis	0.02 RPM	24.79 RPM
bodymap2_thyroid	0.00 RPM	6.67 RPM
bodymap2_white_blood_cells	0.00 RPM	11.03 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4254 was not detected

EST

No EST(s) were mapped for retro_hsap_4254 retrocopy.

TSS

No TSS is located nearby retro_hsap_4254 retrocopy 5' end.

Lab

retro_hsap_4254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000185340	1 retrocopy	retro_hsap_4254 ,
Myotis lucifugus	ENSMLUG00000012081	1 retrocopy	retro_mluc_2597,