RetrogeneDB ID: retro_pabe_1122

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:66190492..66191351(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PTBP1
• Ensembl ID: ENSPPYG00000009289
• Aliases: None
• Description: polypyrimidine tract binding protein 1 [Source:HGNC Symbol;Acc:9583]

Sequence

>retro_pabe_1122
ATGGACGGCATTGTCTCAGAAATAGCAGTTGGTTCAAAGCGGGGATCTGACGAGCTTTTCTCTACTTGTGTCACTAACAG
ACCATTTATCATGAGCAGCAAGTTGGCCTCTGCAGCAAATGGACACGGCAGCAAGAAGTTCAAAGGTGACAGAAGAAGTG
CCGGTGTCCCCTCCAGAGTGACCCACATCCAGAAGCTCCCATCGACGTCACCGAAGGGGAGGTGATTTCCCTGGAGCTGC
CCTTTGGGAATGTCACTAACCTCCTGATGCTGAAGGGGAAAAACCAGGCCTTCATCGAGTTGAGGACGGAGGGGGCTGCC
AACACCGTGGAGAACTACTACACCTCGGTGACGCCCGTGCTGCGTGGCCAGCCCATCTACATCCAGTTCTCCAACCACAA
GGGGCTGAAGACCGACAGCTCTCCCAACCAGGCGCGGGACCTGGCGGCCCTCAGGCCGTGAACTCGGTCCAGTCGGGGAA
CCTGGCCTTGACTGCCCCGGCGGCGGCCGTAGATGCAGGGATGGCGATGGCCGGGCAGAGCCCGGTGCTCAGGATCATCG
TGGAGAACCTCTTCTACCCCATGACCCTGGATGTGCTGCACCAGATTTTCTCCAAGTTCGGCAAAGTGAACACCATCACC
TTCATCAAGGACAACCAGTTCCAGGCCCTGCTGCAGTACGCGGACCCCGAGAACGCCCAGCATGCCAAGCTGTCGCTGGA
CTGGCAGAACACCTACAACGCCTGCCATAACGCTGTGCATTGACTTCTCCAAGCTCACCAGCCTCAACGTCAGGTACAAC
GACAAGAGCAGCGACTACTACGCCCAGACCTGCCCTCCAGGGACAGCCAGCCCTCGCTG

Alignment

ORF - retro_pabe_1122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.3 %
• Parental protein coverage: 53.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDGIVPDIAVGTKRGSDELFSTCVTNGPFIMSSNSASAANGNDSKKFKGDSRSAGVPSRVIHIRKLP-ID
          MDGIV..IAVG.KRGSDELFSTCVTN.PFIMSS..ASAANG..SKKFKGD.RSAGVPSRV.HI.KLP.ID
Retrocopy MDGIVSEIAVGSKRGSDELFSTCVTNRPFIMSSKLASAANGHGSKKFKGDRRSAGVPSRVTHIQKLP<ID

Parental  VTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTD
          VTEGEVISL.LPFG.VTNLLMLKGKNQAFIE..TE.AANT..NYYTSVTPVLRGQPIYIQFSNHK.LKTD
Retrocopy VTEGEVISLELPFGNVTNLLMLKGKNQAFIELRTEGAANTVENYYTSVTPVLRGQPIYIQFSNHKGLKTD

Parental  SSPNQARAQAAL-QAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFG
          SSPNQAR..AAL.QAVNSVQSGNLAL.A.AAAVDAGMAMAGQSPVLRIIVENLFYP.TLDVLHQIFSKFG
Retrocopy SSPNQARDLAAL<QAVNSVQSGNLALTAPAAAVDAGMAMAGQSPVLRIIVENLFYPMTLDVLHQIFSKFG

Parental  TVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDY-T
          .V...ITF.K.NQFQALLQYADP..AQHAKLSLD.QN.YNAC..TL.IDFSKLTSLNV.Y.NDKS.DY..
Retrocopy KV-NTITFIKDNQFQALLQYADPENAQHAKLSLDWQNTYNAC>ITLCIDFSKLTSLNVRY-NDKSSDY<L

Parental  RPDLPSGDSQPSI
          RPDLPS.DSQPS.
Retrocopy RPDLPSRDSQPSL

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
SRP007412_brain_prefrontal_cortex	0.11 RPM	13.49 RPM
SRP007412_cerebellum	0.12 RPM	14.47 RPM
SRP007412_heart	0.09 RPM	9.33 RPM
SRP007412_kidney	0.40 RPM	62.61 RPM
SRP007412_liver	0.34 RPM	32.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1122 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1122 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1122 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122 ,
Pongo abelii	ENSPPYG00000009945	2 retrocopies	retro_pabe_1282, retro_pabe_3576,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,