RetrogeneDB ID: retro_pabe_2963

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:73634117..73634643(-)
• Located in intron of: ENSPPYG00000016769

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPMS2
• Ensembl ID: ENSPPYG00000006553
• Aliases: None
• Description: RNA binding protein with multiple splicing 2 [Source:HGNC Symbol;Acc:19098]

Sequence

>retro_pabe_2963
ATCAGCGGCCTCCCCATGGACACTAAACCCAGAGAACCCTACTTGATCTTCCAGCCGTCCAAGGGGTATGAAGAGTCCCT
AATCAAGCTCACCGCGAGACAGCCTGTTTGTTTTGTGATCTTTGACAGCTGGACAGGAGCAGAAGCGGCCAAAAATGCGC
TGAACGATATTCGCTTAGATCCCGAAAACCCACAGATCATGAGGCTAGAGTTTGCCAAAGCCAACACCAAGATGGCCAAG
AGCAAGCTAATGGCAACTCCAAATCCCACCAACATGCACTCCACCTAGGAACACATTTACTTCATCGCTCGGGACCCCTA
TGACCTGATGGGGGCTGCTCTGATCCCTGCACCCCCAGAGGCCTGGGCCCTTAACCTTTGTACACCACAGAGCTGACCCC
AGCCATCACCCATGCTGCATTCACCTACCCAGCTGCCACTACCATTGCCGCCGCCCTCCATGCCAGGTGCGCTAGTTCCC
TTCCTCTGACACCACCCAGCAAGGATGGAAGTATCGTCAGTTCTGT

Alignment

ORF - retro_pabe_2963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.9 %
• Parental protein coverage: 79.46 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSGLPVDIKPRELYLLFRPFKGYEGSLIKLTARQPVGFVIFDSRAGAEAGKNALNGIRFDPENPQTLRLE
          .SGLP.D.KPRE.YL.F.P.KGYE.SLIKLTARQPV.FVIFDS..GAEA.KNALN.IR.DPENPQ..RLE
Retrocopy ISGLPMDTKPREPYLIFQPSKGYEESLIKLTARQPVCFVIFDSWTGAEAAKNALNDIRLDPENPQIMRLE

Parental  FAKANTKIQLAKESKLMATPNPSNVHPA-LGAHFIARDPYDLMGAALIPASPEAWA-PYPLYTTELTPAI
          FAKANTK......SKLMATPNP.N.H.......FIARDPYDLMGAALIPA.PEAWA.P.PLYTTELTPAI
Retrocopy FAKANTKM---AKSKLMATPNPTNMHST*EHIYFIARDPYDLMGAALIPAPPEAWA<P*PLYTTELTPAI

Parental  SHAAFTYPAATAAAAALHA-QVRWYPSSDTTQQGWKYRQFC
          .HAAFTYPAAT..AAALHA.QVR..PSSDTTQQGWKYRQFC
Retrocopy THAAFTYPAATTIAAALHA<QVR*FPSSDTTQQGWKYRQFC

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	0.83 RPM	0.94 RPM
SRP007412_cerebellum	0.24 RPM	0.00 RPM
SRP007412_heart	3.25 RPM	6.14 RPM
SRP007412_kidney	1.46 RPM	3.05 RPM
SRP007412_liver	0.43 RPM	0.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2963 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2963 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3613
Pan troglodytes	retro_ptro_2441
Gorilla gorilla	retro_ggor_2438
Macaca mulatta	retro_mmul_1837

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011037	1 retrocopy	retro_btau_1674,
Callithrix jacchus	ENSCJAG00000005200	2 retrocopies	retro_cjac_1775, retro_cjac_298,
Dipodomys ordii	ENSDORG00000004025	1 retrocopy	retro_dord_438,
Homo sapiens	ENSG00000166831	2 retrocopies	retro_hsap_2513, retro_hsap_3613,
Gorilla gorilla	ENSGGOG00000008984	1 retrocopy	retro_ggor_2438,
Loxodonta africana	ENSLAFG00000018725	6 retrocopies	retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550, retro_lafr_859,
Macaca mulatta	ENSMMUG00000013270	1 retrocopy	retro_mmul_1837,
Monodelphis domestica	ENSMODG00000010487	1 retrocopy	retro_mdom_571,
Mus musculus	ENSMUSG00000032387	9 retrocopies	retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562, retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys	ENSNLEG00000012505	1 retrocopy	retro_nleu_2209,
Otolemur garnettii	ENSOGAG00000026017	1 retrocopy	retro_ogar_3254,
Pongo abelii	ENSPPYG00000006553	1 retrocopy	retro_pabe_2963 ,
Pan troglodytes	ENSPTRG00000007165	2 retrocopies	retro_ptro_1458, retro_ptro_2441,
Sus scrofa	ENSSSCG00000004549	1 retrocopy	retro_sscr_851,
Ictidomys tridecemlineatus	ENSSTOG00000010055	2 retrocopies	retro_itri_1512, retro_itri_556,
Tarsius syrichta	ENSTSYG00000008996	3 retrocopies	retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus	ENSTTRG00000011840	3 retrocopies	retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,