RetrogeneDB ID: retro_pabe_2235

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:104489775..104490502(+)
• 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_2235
ATGGATGATACAAGAGCTTCACTTGATACGGAAGAGTATCCCAATACTGAGGTCAGGAAAACCGAGTACGAACTGTGGAA
GAATGGCAAGACAAGTGAGTGAACGGCAATACTGCTTTTCATCAAGAACAAAGACATCAGCTATTGAAGAAGCATTTGGA
TACTTTTCTTAAAGGTGAGAGTAGACCGAAGGTATTTTTTCCTCCTTGTTGAGATGAAATGGTTTACAGACCAAGGACAC
AATGTAGTTGGTGTATAAATCAGTGCACTTGGGAGAATTACGAGAATTTTTTACAGAGCAGAATCTTTCTTACTCAAAAG
AACCAATTAGCAAAGTTCCTGAAGCCAAAGTATTTAAGAGTTCTTCAGAGAACATTTCATTGTACTGTTGCAGCATTTTT
TATCTTCCCCAAACACATATCGACAAATTTGACAGAATTTGGGATAGAGGAGCACTGGCTGCCATTAATCTAGGAGATTT
CAAACACTATGCAGATACAATGTTGTCCCTCCTGGGAAAAGGGTTTCAGTACCTCGTGTGTGTTCTTTCTTATGACCCAA
CTAAACATGCAGGCCCACTATCTTATGTTCCACATGCTGAAATTGAAAGGTTGTTCAGTACAATATGCAATATTCATTGT
CTTGAGAAGATTGATGCTTTTGAAGAACAACATGAAAGTTGGCAAATTGACTACATTTTTGAAAAGTTATATCTACTTAC
AGAAAAG

Alignment

ORF - retro_pabe_2235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDGIRTSLDIEEYSDTEVQK-NQVLTLEEWQDKWVNGNTAFHQEQGHRLLKKHLDTFLKGES-GLRVFFP
          MD..R.SLD.EEY..TEV.K.N.V.T.EEWQDK.VNGNTAFHQEQ.H.LLKKHLDTFLKGES...R.FF.
Retrocopy MDDTRASLDTEEYPNTEVRK<NRVRTVEEWQDK*VNGNTAFHQEQRHQLLKKHLDTFLKGES>DRRYFFL

Parental  LCGKAVEMKWFADRGHSVVGVEIS-ELG-IREFFTEQNLSYSEEPVTEIPGTKIFKSSSGNISLYCCSIF
          L....VEMKWF.D.GH.VVGV.IS..LG..REFFTEQNLSYS.EP....P..K.FKSSS.NISLYCCSIF
Retrocopy L----VEMKWFTDQGHNVVGV*IS>HLGELREFFTEQNLSYSKEPISKVPEAKVFKSSSENISLYCCSIF

Parental  DLPRTNIGKFDMIWDRGALVAINPGDRKCYADTMLSLLGKKFQYLLCVLSYDPTKHPGPPFYVPHAEIER
          .LP.T.I.KFD.IWDRGAL.AIN.GD.K.YADTMLSLLGK.FQYL.CVLSYDPTKH.GP..YVPHAEIER
Retrocopy YLPQTHIDKFDRIWDRGALAAINLGDFKHYADTMLSLLGKGFQYLVCVLSYDPTKHAGPLSYVPHAEIER

Parental  LFGKICNIHCLEKVDAFEERHKSWGIDYLFEKLYLLTEK
          LF..ICNIHCLEK.DAFEE.H.SW.IDY.FEKLYLLTEK
Retrocopy LFSTICNIHCLEKIDAFEEQHESWQIDYIFEKLYLLTEK

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	0.11 RPM	21.84 RPM
SRP007412_cerebellum	0.36 RPM	13.50 RPM
SRP007412_heart	0.09 RPM	6.86 RPM
SRP007412_kidney	0.17 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_2235 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2235 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2781
Pan troglodytes	retro_ptro_1882
Gorilla gorilla	retro_ggor_1938
Macaca mulatta	retro_mmul_1445

---

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,