RetrogeneDB ID: retro_pabe_2402

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3_random:1228476..1228954(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDSP2
• Ensembl ID: ENSPPYG00000004711
• Aliases: None
• Description: CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2 [Source:HGNC Symbol;Acc:17077]

Sequence

>retro_pabe_2402
ATGGAACAAGTCTCCATCATCACCCAGGCATGGAGGGAAGATGCCCTGGTCCTTACCAAGCAAGTCCTGGTTTCCAAAGT
GCTCTCTGAAGAGGTCTCATGATTGTCACACCTTAGAAGGCCCTTTCTGCTCTTCTTGCACCCAGCATGTTGGCCAGTCA
CGTTCCCCTGCTGAGCTCTCCACACATAAGGAGGAAGTCAACACCATTGCTAAGTCAATTCAGCTCCAGAGTCTCCAGTA
TCAGTTTTATCAGATCCCAGGAACCTGCCTGCTCCCAGAGGTGACAGAGAAAAATCAAGGAACGATCTGTATGGGCACTG
ACTTGCATGAAACCCTTGTGCCTAGCTCCTTGAAACATTCAGCAATGCTGACTGCCTAATGCCTGTAGAGATTGAGGAGA
CCAGGCACCAGATCCATTTGCTCATGAGCCTTATATGGATGAGTTCCTGAGATGACAGGAGGACTGCTTAAATGTGTT

Alignment

ORF - retro_pabe_2402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.98 %
• Parental protein coverage: 56.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEHGSIITQARREDALVLTKQGLVSK-SSPKKPRGRNIFKALFCCFRAQHVGQSSSSTELAAYKEEANTI
          ME..SIITQA.REDALVLTKQ.LVSK..S.K...........FC....QHVGQS.S..EL...KEE.NTI
Retrocopy MEQVSIITQAWREDALVLTKQVLVSK>CSLKRSHDCHTLEGPFCSSCTQHVGQSRSPAELSTHKEEVNTI

Parental  AKSDLLQCLQYQFYQIPGTCLLPEVTEEDQGRICVVIDLDETLVHSSFK-PINNADFIVPIEIEGTTHQV
          AKS..LQ.LQYQFYQIPGTCLLPEVTE..QG.IC...DL.ETLV.SS.K....NAD...P.EIE.T.HQ.
Retrocopy AKSIQLQSLQYQFYQIPGTCLLPEVTEKNQGTICMGTDLHETLVPSSLK<TFSNADCLMPVEIEETRHQI

Parental  YVL-KRPYVDEFLR-RMGELFECV
          ..L...PY.DEFLR...G.L..CV
Retrocopy HLL<HEPYMDEFLR<MTGGLLKCV

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	10.78 RPM
SRP007412_cerebellum	0.85 RPM	16.42 RPM
SRP007412_heart	0.00 RPM	9.99 RPM
SRP007412_kidney	0.27 RPM	25.49 RPM
SRP007412_liver	0.03 RPM	10.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2402 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2402 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006503	2 retrocopies	retro_cjac_3087, retro_cjac_919,
Homo sapiens	ENSG00000175215	2 retrocopies	retro_hsap_4315, retro_hsap_4319,
Macaca mulatta	ENSMMUG00000005321	2 retrocopies	retro_mmul_2208, retro_mmul_764,
Mus musculus	ENSMUSG00000078429	1 retrocopy	retro_mmus_612,
Nomascus leucogenys	ENSNLEG00000017164	2 retrocopies	retro_nleu_1741, retro_nleu_3079,
Petromyzon marinus	ENSPMAG00000009544	2 retrocopies	retro_pmar_20, retro_pmar_27,
Pongo abelii	ENSPPYG00000004711	14 retrocopies	retro_pabe_1708, retro_pabe_1739, retro_pabe_1740, retro_pabe_1742, retro_pabe_1746, retro_pabe_1762, retro_pabe_2402 , retro_pabe_2592, retro_pabe_3202, retro_pabe_3205, retro_pabe_3221, retro_pabe_3237, retro_pabe_3554, retro_pabe_3578,
Pan troglodytes	ENSPTRG00000005155	7 retrocopies	retro_ptro_2587, retro_ptro_2589, retro_ptro_2590, retro_ptro_2592, retro_ptro_2594, retro_ptro_2958, retro_ptro_3054,