RetrogeneDB ID: retro_pabe_662

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10_random:36608402..36609461(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000025933
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_662
CTGTGGCCCACTTCGGTGGACCCAGCGCTGAGGCGGCGGCGGCGAGGCCCAAGAAATAAGAAGCAGGGCTGGCGGTGGCT
TGCTCAGGAGCCGCTGGGGCTGGAGGTTGACCAGTTCCTGGAAGACGTGCGGCTACAGGAGCGCACGAGCGGTGGCTTGC
TGTCAGAGGCCCCAAATGAAAAACTCTTCTTCGTGGACACTGGCTCCAAGGAAAAAGGGCTGACAAAGAAGAGAACCAAA
GTCCAGAAGAAGTCACTGCTTCTCAAGAAACCCCTTCGGGTTGACCTCGTCCTCGAGAACACATCCAAAGTCCCTGCTCC
CAAAGACGTCCTCGCCCACCAGGTCCCCAGCGCCAAGAAGCTCAGGCGGATGGAGCAGCTATGGGAGAAGCTGGCCAAGC
AGGGCGAGCTGCCCCGGGAGGTGCGCAGGGCCCAGGCCCGGCTCCTCAACCCTCCCGCGGCCAGGGCCAAGCCCGGGCCC
CAGGACACCGTGGAGCGGCCCTTCTACGACCTCTGGGCCTCAGACAACCCCCTGGACAGGCCGTTGGTTGGCCAGGATGA
GTTTTTCCTGGAGCAGACCAAGAAGAAAGGAGTGAAGCGGCCACCACGCCTGCACACCAAGCCGTCCCAGGCACCCGCCG
TGGAGGTGGCGCCTGCCGGAGCTTCCTACAACCCGTCCTTTGAAGACCACCAGGCCCTGCTCTCAGCGGCCCACGAGGTG
GAGTTGCAGCGGCAGAAAGAGGCGGAGAAGCTGGAGCGGCAGCTGGCCCTGCCCGCCACGGAGCAGGCCGCCACCCAGGA
GTCCACGTTCCAGGAGCTGTGCGAGGGGCTGCTGGAGGAGTCGGATGGTGAGGGGGAGCCAGGCCAGGGCGAGGCGCCAG
AGGCTGGGGATGCCGAGGTCGGTCCCATGCCCGCTCGCCTGGCCACCACAGAGAAGAAGACGGAGCAGCAGCGGCGGCGG
GAGAAGGCTGCGCTCAGGCTGCGGGTACAGCAGGCCGCGTTGCTGGCCGCCCGGCTCCGGCACCAGGAGCTGTTCCGGCT
GCGCGGGATCAAGGCCCAG

Alignment

ORF - retro_pabe_662 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.32 %
• Parental protein coverage: 79.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRPTSVDPALRRRRRGPRNKKRGWRRLAQEPLGLEVDQFLEDVRLQERTSGGLLSEAPNEKLFFVDTGSK
          L.PTSVDPALRRRRRGPRNKK.GWR.LAQEPLGLEVDQFLEDVRLQERTSGGLLSEAPNEKLFFVDTGSK
Retrocopy LWPTSVDPALRRRRRGPRNKKQGWRWLAQEPLGLEVDQFLEDVRLQERTSGGLLSEAPNEKLFFVDTGSK

Parental  EKGLTKKRTKVQKKSLLLKKPLRVDLILENTSKVPAPKDVLAHQVPNAKKLRRKEQLWEKLAKQGELPRE
          EKGLTKKRTKVQKKSLLLKKPLRVDL.LENTSKVPAPKDVLAHQVP.AKKLRR.EQLWEKLAKQGELPRE
Retrocopy EKGLTKKRTKVQKKSLLLKKPLRVDLVLENTSKVPAPKDVLAHQVPSAKKLRRMEQLWEKLAKQGELPRE

Parental  VRRAQARLLNPPAARAKPGPQDTVERPFYDLWASDNPLDRPLVGQDEFFLEQTKKKGVKRPQRLHTKPSQ
          VRRAQARLLNPPAARAKPGPQDTVERPFYDLWASDNPLDRPLVGQDEFFLEQTKKKGVKRP.RLHTKPSQ
Retrocopy VRRAQARLLNPPAARAKPGPQDTVERPFYDLWASDNPLDRPLVGQDEFFLEQTKKKGVKRPPRLHTKPSQ

Parental  APAVEVAPAGASYNPSFEDHQTLLSAAHEVELQRQKEAEKLERQLALPATEQAATQESTFQELCEGLLEE
          APAVEVAPAGASYNPSFEDHQ.LLSAAHEVELQRQKEAEKLERQLALPATEQAATQESTFQELCEGLLEE
Retrocopy APAVEVAPAGASYNPSFEDHQALLSAAHEVELQRQKEAEKLERQLALPATEQAATQESTFQELCEGLLEE

Parental  SDGEGEPGQGEGPEAGDAEVGPMPARLATTEKKTEQQRRREKVARRLRVQQAALLAARLRHQELFRLLGI
          SDGEGEPGQGE.PEAGDAEVGPMPARLATTEKKTEQQRRREK.A.RLRVQQAALLAARLRHQELFRL.GI
Retrocopy SDGEGEPGQGEAPEAGDAEVGPMPARLATTEKKTEQQRRREKAALRLRVQQAALLAARLRHQELFRLRGI

Parental  KDQ
          K.Q
Retrocopy KAQ

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	3.15 RPM	16.64 RPM
SRP007412_cerebellum	1.95 RPM	12.77 RPM
SRP007412_heart	2.56 RPM	15.20 RPM
SRP007412_kidney	5.34 RPM	31.85 RPM
SRP007412_liver	2.88 RPM	21.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_662 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_662 has 0 orthologous retrocopies within eutheria group .

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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,