RetrogeneDB ID: retro_pabe_3786

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:84532870..84533538(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPMT
• Ensembl ID: ENSPPYG00000016263
• Aliases: None
• Description: thiopurine S-methyltransferase [Source:RefSeq peptide;Acc:NP_001125496]

Sequence

>retro_pabe_3786
ATTGAAGAGTATTCCGATACTGAGGTACAGAAACACCAAGTACTAAGTCTGGAAGCATGGCAAGACAAGCTTATTAAAGC
ATTTGGATACTTTTCATAAAGGTGAGAGTGGACTGATGATGTTTTTTCCTCTATATGGAAAAGTATTAACAGTTGAGATG
AAATGGTTTCCATACCAGGGACACAGTGCAGTTGGTGTGAAAATCAGTTAACTTGAGATACAAGAATGTTTTACAGAGCA
AATCTTTCTTACTCAGAAGAGCCAATCACTAAAATTCCTGAAACCAAATATATAAGAGTTCTTCAGGGAATATTTCATTG
TACTGTTGCAGCATTTTTTATCTTCCCAGAACAAATATTGACAAATTTGACAGGATTTGGAATAGAGGAGCATTAGTTAC
CATTAATCCAGGTGGATTGTGAATGCTCTGCAAGTATAATGTCGTTCCTCCTGAGAAAACGGTTTCAGTACCTCATGTGT
GTTCTTTCTTATGATTCAAGTAAAAACATGCAGCCCACCATTTTTATGTTCCACATGCTTAAATTGAAAGGTTGTTTGGT
ACAACATGCAGTATTTATTGTCCTGGAAATGCTGATGCTTTTGAAGAACAACATAAAAGTTGGGGAATTGACTACATTTT
TGGAAAGATAGATCTACTTACAGAAAAG

Alignment

ORF - retro_pabe_3786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.79 %
• Parental protein coverage: 89.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LEEWQDKWVNGNTAFHQE-QGHRLLKKHLDTFLKGESGLRVFFPLCGKA--VEMKWFADRGHSVVGVEIS
          .EE..D..V........E..G...L.KHLDTF.KGESGL..FFPL.GK...VEMKWF...GHS.VGV.IS
Retrocopy IEEYSDTEVQKHQVLSLE>HGKTSLLKHLDTFHKGESGLMMFFPLYGKVLTVEMKWFPYQGHSAVGVKIS

Parental  ELGIREFFTEQ-NLSYSEEPVTEIPGTK-IFKSSSGNISLYCCSIFDLPRTNIGKFDMIWDRGALVAINP
          .L.I.E.FTEQ.NLSYSEEP.T.IP.TK.I.KSSSGNISLYCCSIF.LPRTNI.KFD.IW.RGALV.INP
Retrocopy *LEIQECFTEQ<NLSYSEEPITKIPETK<IYKSSSGNISLYCCSIFYLPRTNIDKFDRIWNRGALVTINP

Parental  G-DRKCYADTMLSLLGKKFQYLLCVLSYDPTKHP-GPPF-YVPHAEIERLFGKICNIHCLEKVDAFEERH
          G.D..C.A..M..LL.K.FQYL.CVLSYD..K....PPF.YVPHA.IERLFG..C.I.C....DAFEE.H
Retrocopy G>DCECSASIMSFLLRKRFQYLMCVLSYDSSKNM>SPPF>YVPHA*IERLFGTTCSIYCPGNADAFEEQH

Parental  KSWGIDYLFEKLYLLTEK
          KSWGIDY.F.K..LLTEK
Retrocopy KSWGIDYIFGKIDLLTEK

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	21.84 RPM
SRP007412_cerebellum	0.00 RPM	13.50 RPM
SRP007412_heart	0.00 RPM	6.86 RPM
SRP007412_kidney	0.00 RPM	38.35 RPM
SRP007412_liver	0.00 RPM	15.97 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3786 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3786 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3786 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_4192
Macaca mulatta	retro_mmul_2609

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008676	27 retrocopies	retro_chof_1029, retro_chof_1047, retro_chof_1184, retro_chof_1209, retro_chof_1425, retro_chof_1451, retro_chof_1483, retro_chof_1498, retro_chof_168, retro_chof_1830, retro_chof_1946, retro_chof_195, retro_chof_2039, retro_chof_2203, retro_chof_2543, retro_chof_2562, retro_chof_2649, retro_chof_330, retro_chof_503, retro_chof_626, retro_chof_637, retro_chof_684, retro_chof_743, retro_chof_761, retro_chof_78, retro_chof_79, retro_chof_921,
Callithrix jacchus	ENSCJAG00000006906	2 retrocopies	retro_cjac_1617, retro_cjac_4192,
Cavia porcellus	ENSCPOG00000005295	1 retrocopy	retro_cpor_666,
Dasypus novemcinctus	ENSDNOG00000004842	1 retrocopy	retro_dnov_965,
Homo sapiens	ENSG00000137364	4 retrocopies	retro_hsap_1884, retro_hsap_2781, retro_hsap_4835, retro_hsap_4868,
Gorilla gorilla	ENSGGOG00000016155	4 retrocopies	retro_ggor_1381, retro_ggor_1938, retro_ggor_3014, retro_ggor_3041,
Loxodonta africana	ENSLAFG00000011632	1 retrocopy	retro_lafr_438,
Macaca mulatta	ENSMMUG00000016627	3 retrocopies	retro_mmul_1445, retro_mmul_2576, retro_mmul_2609,
Mus musculus	ENSMUSG00000021376	1 retrocopy	retro_mmus_2738,
Nomascus leucogenys	ENSNLEG00000001548	4 retrocopies	retro_nleu_1806, retro_nleu_2001, retro_nleu_2710, retro_nleu_682,
Oryctolagus cuniculus	ENSOCUG00000003854	2 retrocopies	retro_ocun_1255, retro_ocun_1370,
Otolemur garnettii	ENSOGAG00000007738	2 retrocopies	retro_ogar_1972, retro_ogar_701,
Pongo abelii	ENSPPYG00000016263	4 retrocopies	retro_pabe_1563, retro_pabe_2235, retro_pabe_3758, retro_pabe_3786 ,
Pan troglodytes	ENSPTRG00000017756	5 retrocopies	retro_ptro_1265, retro_ptro_1882, retro_ptro_3217, retro_ptro_3218, retro_ptro_3243,