RetrogeneDB ID: retro_pabe_1270

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:91720901..91722021(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLTSCR2
• Ensembl ID: ENSPPYG00000010181
• Aliases: None
• Description: glioma tumor suppressor candidate region gene 2 [Source:HGNC Symbol;Acc:4333]

Sequence

>retro_pabe_1270
ATGGCGGCAGGAGGCGGTGGCGTTGGTGGGAAGCACAGCTCGAAAAGCGATGACGATTCCGGTTTCCTGGGGCTGCGGCC
CATTTCGGTGGACCCAGCGCTGAGGCAGCGGTGGCAAGGCCCAAGAAATAAGAAGCGGGGCTGGCGGCGGCTTGCTCAGG
AGCCGCTGGGGCTGGAGGTTGACCAGTTCCTGGAAGACGTGCGGCTACAGGAGCGCACGAGTGGCAGCTTGTTGTCAGAG
GCCCCAAATGAAAAACTTCTTCGTGGACACCGGCTCCAAGGAAAAAGGGCTAAGAAGAGAACCAAAGTCCAGAAGAAGTC
ACTGCTTCTCAAGAAACCCCTTCGAGTTGACCTCATCCTTGAGAACACATCCAAAGTCCCTGCCCCCAAAGACGTCCTCG
CCCACCAGGTCCCCAACGCCAAGAAGCTCAGGCGGAAGGAGCAGCTATGGGAGAAGCTGGCCAAGCAGCGCGAGCTGCCC
CGGGAGGTGCGCAGGGCCCAGGCCCAGCTCCTCAACCCTCCCACAGCCAGGGCCAAGCCCGGGCCCCAGGACACCGTGGA
GCGGCCCTTCTACGACCTCTGGGTCTCAGACAACCCCCTGGACAGGCCGTTGTTTGGCCAGGATGAGCTTTTCCTGGAGC
AGACCAAGAAGAAAGGAGTGAAGCGGCCACCACGCCTGCACACCAAGCCGTCCCAGGCACCCGCCGTGGAGGTGGCGCCT
GCCGGCGCTTCCTACAACCCGTCCTTTGAAGACCACCAGACCCTGCTCTCAGCGGCCCACGAGGTGGAGTGGCAGCGGTA
GAAGGAGGCGGAGAAGCCGGAGCGGCAGCTGGCCCTGCCCGCCACAGAGCAGGCCGCCACCCAGGAGTCCACGTTCCAGG
TAGCTGTGCGAGGGGCTGCTGGAGGAGTCGCATGGTGAGGGGGAGCCAGGCCAGGGCGAGGGGCCGGAGGCTGGGGATGC
CGAGGTCTGTCCCACGCCAGCCCGCCTGGCCGCCACAGAGAAGAAGACGGAGCAGCAGCGGCGGCGGGAGAAGGCTGCGC
GCAGGCTGCGGGTACAGCAGGCCGCGTTGCGGGCTGCCCGGCTCCGGCGCCAGGAGGTGTTCTTGCTGCGCGGGATCAAG

Alignment

ORF - retro_pabe_1270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.59 %
• Parental protein coverage: 84.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGDSGVGGKHSSKSDADSGFLGLRPTSVDPALRRRRRGPRNKKRGWRRLAQEPLGLEVDQFLEDVRLQ
          MAAG..GVGGKHSSKSD.DSGFLGLRP.SVDPALR.R..GPRNKKRGWRRLAQEPLGLEVDQFLEDVRLQ
Retrocopy MAAGGGGVGGKHSSKSDDDSGFLGLRPISVDPALRQRWQGPRNKKRGWRRLAQEPLGLEVDQFLEDVRLQ

Parental  ERTSGGLLSEAPNEKLFFVDTGSKEKGLTKK-RTKVQKKSLLLKKPLRVDLILENTSKVPAPKDVLAHQV
          ERTSG.LLSEAPNEKL.....G....G...K.RTKVQKKSLLLKKPLRVDLILENTSKVPAPKDVLAHQV
Retrocopy ERTSGSLLSEAPNEKLL---RGHRLQGKRAKKRTKVQKKSLLLKKPLRVDLILENTSKVPAPKDVLAHQV

Parental  PNAKKLRRKEQLWEKLAKQGELPREVRRAQARLLNPPAARAKPGPQDTVERPFYDLWASDNPLDRPLVGQ
          PNAKKLRRKEQLWEKLAKQ.ELPREVRRAQA.LLNPP.ARAKPGPQDTVERPFYDLW.SDNPLDRPL.GQ
Retrocopy PNAKKLRRKEQLWEKLAKQRELPREVRRAQAQLLNPPTARAKPGPQDTVERPFYDLWVSDNPLDRPLFGQ

Parental  DEFFLEQTKKKGVKRPQRLHTKPSQAPAVEVAPAGASYNPSFEDHQTLLSAAHEVELQRQKEAEKLERQL
          DE.FLEQTKKKGVKRP.RLHTKPSQAPAVEVAPAGASYNPSFEDHQTLLSAAHEVE.QR.KEAEK.ERQL
Retrocopy DELFLEQTKKKGVKRPPRLHTKPSQAPAVEVAPAGASYNPSFEDHQTLLSAAHEVEWQR*KEAEKPERQL

Parental  ALPATEQAATQESTFQE-LCEGLLEESDGEGEPGQGEGPEAGDAEVGPMPARLATTEKKTEQQRRREKVA
          ALPATEQAATQESTFQ..LCEGLLEES.GEGEPGQGEGPEAGDAEV.P.PARLA.TEKKTEQQRRREK.A
Retrocopy ALPATEQAATQESTFQV>LCEGLLEESHGEGEPGQGEGPEAGDAEVCPTPARLAATEKKTEQQRRREKAA

Parental  RRLRVQQAALLAARLRHQELFRLLGIK
          RRLRVQQAAL.AARLR.QE.F.L.GIK
Retrocopy RRLRVQQAALRAARLRRQEVFLLRGIK

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	0.00 RPM	16.64 RPM
SRP007412_cerebellum	0.00 RPM	12.77 RPM
SRP007412_heart	0.03 RPM	15.20 RPM
SRP007412_kidney	0.07 RPM	31.85 RPM
SRP007412_liver	0.00 RPM	21.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1270 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1270 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1270 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1528
Pan troglodytes	retro_ptro_1035

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000105373	1 retrocopy	retro_hsap_1528,
Macropus eugenii	ENSMEUG00000002525	2 retrocopies	retro_meug_1136, retro_meug_1713,
Nomascus leucogenys	ENSNLEG00000003143	1 retrocopy	retro_nleu_1937,
Pongo abelii	ENSPPYG00000010181	3 retrocopies	retro_pabe_1270 , retro_pabe_653, retro_pabe_662,
Pan troglodytes	ENSPTRG00000011215	1 retrocopy	retro_ptro_1035,
Rattus norvegicus	ENSRNOG00000013023	1 retrocopy	retro_rnor_1107,