RetrogeneDB ID: retro_pabe_653

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10_random:10839777..10840462(-)
• 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_653
CAGCTATGGGAGAAGCTGGCAAAGCAGGGCGAGCTGCCCCGGGAGGTGCGCAGGGCCCAGGCCCGGCTCCTCCACCCCTC
CCGCGGCCAGGGCCAAGCCCGGGCCCCAGGACACCGTGGAGCGGCCCTTCTACGACCTCTGGGCCTCAGACAACCCCCTG
GACAGGCCGTTGGTTGGCCAGGATGAGTTTTTCCTGGAGCAGACCAAGAAGAAAGGAGTGAAGCGGCCACCACGCCTGCA
CACCAAGCCGTCCCAGGCACCCGCCGTGGAGGTGGCGCCTGCCGGAGCTTCCTACAACCCGTCCTTTGAAGACCACCAGG
CCCTGCTCTCAGCGGCCCACGAGGTGGAGTTGCAGCGGCAGAAGGAGGCGAAGAAGATGGAGCGGCAGCTGGCCCTGCCC
GCCACGGAGCAGGCCGCCACCCAGGAGTCCACGTTCCAGGAGCTGTGCGAGGGGCTGCTGGAGGAGTCGGATGGTGAGGG
GGAGCCAGGCCAGGGCGAGGCGCCAGAGGCTGGGGATGCCGAGGTCGGTCCCATGCCCGCTTGCCTGGCCACCACAGAGA
AGAAGACGGAGCAGCAGCGGCGGCCGGAGAAGGCTGCGCTCAGGCTGCGGGTACAGCAGGCCGCGTTGCTGGCCGCCCGG
CTCCGGCACCAGGAGCTGTTCCGGCTGCGCGGGATCAAGGCCCAG

Alignment

ORF - retro_pabe_653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.32 %
• Parental protein coverage: 51.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLWEKLAKQGELPREVRRAQARLLN-PPAARAKPGPQDTVERPFYDLWASDNPLDRPLVGQDEFFLEQTK
          QLWEKLAKQGELPREVRRAQARLL..PPAARAKPGPQDTVERPFYDLWASDNPLDRPLVGQDEFFLEQTK
Retrocopy QLWEKLAKQGELPREVRRAQARLLH>PPAARAKPGPQDTVERPFYDLWASDNPLDRPLVGQDEFFLEQTK

Parental  KKGVKRPQRLHTKPSQAPAVEVAPAGASYNPSFEDHQTLLSAAHEVELQRQKEAEKLERQLALPATEQAA
          KKGVKRP.RLHTKPSQAPAVEVAPAGASYNPSFEDHQ.LLSAAHEVELQRQKEA.K.ERQLALPATEQAA
Retrocopy KKGVKRPPRLHTKPSQAPAVEVAPAGASYNPSFEDHQALLSAAHEVELQRQKEAKKMERQLALPATEQAA

Parental  TQESTFQELCEGLLEESDGEGEPGQGEGPEAGDAEVGPMPARLATTEKKTEQQRRREKVARRLRVQQAAL
          TQESTFQELCEGLLEESDGEGEPGQGE.PEAGDAEVGPMPA.LATTEKKTEQQRR.EK.A.RLRVQQAAL
Retrocopy TQESTFQELCEGLLEESDGEGEPGQGEAPEAGDAEVGPMPACLATTEKKTEQQRRPEKAALRLRVQQAAL

Parental  LAARLRHQELFRLLGIKDQ
          LAARLRHQELFRL.GIK.Q
Retrocopy LAARLRHQELFRLRGIKAQ

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	0.00 RPM	15.20 RPM
SRP007412_kidney	0.00 RPM	31.85 RPM
SRP007412_liver	0.06 RPM	21.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_653 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_653 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,