RetrogeneDB ID: retro_pabe_1742

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1_random:3379141..3379635(-)
• 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_1742
ATGGAACAAGGCTCCATCATCACCCAGGCATGGAGGGAAGATGCCCTGGTCCTTACCAAGCAAGGCCTGGTTTCCAAAGT
GCTCTCCGAAGAGGCCTCATGTTTGTCACACCTTAGAAGGCCCTTTTCTGCTCTTCTTGCACCCAGCATGTTGGCCAGTC
ACGTTCCCCTGCTGAGCTCTCCACACATAAGGAGGAAGTCAACACCATTGCTAAGTCGGATCAGCTCCAGGGTCTCCAGT
TTCAGTTTTATCAGATCCCAGGAACCTGCCTGCTCCCAGAGGTGACAGAGAAAAATCAAGGAAGGATCTGTACGGTCACT
GGCTTGGATGAAACCATTGTGCATAGCTCCTTGAAGCCATTCAGCAATGCTGACTGCCTAATGCCTGTAGAGATTGAGGG
GACCAGGCACCAGATCCTTTTGCTCATGAGGTCTTATATAGATGAGTTCCTGAGATGACAGGAGGAACTGCTTAAATGTG
TTTTTTTCATTGCT

Alignment

ORF - retro_pabe_1742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.47 %
• Parental protein coverage: 58.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEHGSIITQARREDALVLTKQGLVSK-SSPKKPRGRNIFK-ALFCCFRAQHVGQSSSSTELAAYKEEANT
          ME.GSIITQA.REDALVLTKQGLVSK..SPK.P........ALFC....QHVGQS.S..EL...KEE.NT
Retrocopy MEQGSIITQAWREDALVLTKQGLVSK>CSPKRPHVCHTLE>ALFCSSCTQHVGQSRSPAELSTHKEEVNT

Parental  IAKSDLLQCLQYQFYQIPGTCLLPEVTEEDQGRICVVIDLDETLVHSSFKPINNADFIVPIEIEGTTHQV
          IAKSD.LQ.LQ.QFYQIPGTCLLPEVTE..QGRIC.V..LDET.VHSS.KP..NAD...P.EIEGT.HQ.
Retrocopy IAKSDQLQGLQFQFYQIPGTCLLPEVTEKNQGRICTVTGLDETIVHSSLKPFSNADCLMPVEIEGTRHQI

Parental  YVLKRPYVDEFLRRMGELFECVLFTA
          ..L.R.Y.DEFLR...EL..CV.F.A
Retrocopy LLLMRSYIDEFLR*QEELLKCVFFIA

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	0.97 RPM	16.42 RPM
SRP007412_heart	0.00 RPM	9.99 RPM
SRP007412_kidney	0.43 RPM	25.49 RPM
SRP007412_liver	0.55 RPM	10.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1742 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1742 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,