RetrogeneDB ID: retro_pabe_2965

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:74539911..74540277(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXN
• Ensembl ID: ENSPPYG00000019491
• Aliases: None
• Description: thioredoxin [Source:RefSeq peptide;Acc:NP_001125903]

Sequence

>retro_pabe_2965
TTGAAAATGTACGTAAGGGTCCTTAGGGTCACTTGTCGGACTCTAGTACCCAAAACAGTGAAGCAGGTGAAAAGCAACAT
GCTTCTCAGGAAGCCTCGACAGCGCAAGAGATAAACTCATAGCAGTTGTCTCTTCAGACTCGTGGTGCAGGCCTTGCAAA
ATGATCAAGCCTTTCTTGCATTCTCTCTCTGAAAAGTATACCAGAGTGGTGTTCTTTGAGGTAGATATAGATGACTGTCA
GGATGTTACTTCAGTGTGGAAGTCTAATGCATGCCAACTTTCCACTTTTTAAAAATGGAATAAAAGGTGAGTGAATTTTC
TGGAGCTAACAAAGGAAAATTTGAAGGCACCATTAATGAATTAATC

Alignment

ORF - retro_pabe_2965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.52 %
• Parental protein coverage: 55.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LDPFPSVLTAARQTPAAKMVKQI-ESKTAFQEA-LDAAGDKLVVVDFSATWCGPCKMIKPFFHSLSEKYS
          L.....VL.....T...K.VKQ..E...A.QEA.LD.A.DKL..V..S..WC.PCKMIKPF.HSLSEKY.
Retrocopy LKMYVRVLRVTCRTLVPKTVKQV<EKQHASQEA<LDSARDKLIAVVSSDSWCRPCKMIKPFLHSLSEKYT

Parental  NVIFLEVDVDDCQDVAS-ECEVKCMPTFQFFKKGQKVGEFSGANKEKLEATINELV
          .V.F.EVD.DDCQDV.S...EV.CMPTF.F.K...KV.EFSGANK.K.E.TINEL.
Retrocopy RVVFFEVDIDDCQDVTS<SVEV*CMPTFHFLKME*KVSEFSGANKGKFEGTINELI

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	45.12 RPM
SRP007412_cerebellum	0.00 RPM	47.30 RPM
SRP007412_heart	0.00 RPM	21.98 RPM
SRP007412_kidney	0.00 RPM	76.90 RPM
SRP007412_liver	0.00 RPM	62.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2965 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2965 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2965 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3614
Pan troglodytes	retro_ptro_2444
Gorilla gorilla	retro_ggor_2440

---

Parental genes homology:

Parental genes homology involve 32 parental genes, and 140 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013018	3 retrocopies	retro_acar_112, retro_acar_121, retro_acar_122,
Ailuropoda melanoleuca	ENSAMEG00000018017	3 retrocopies	retro_amel_1559, retro_amel_211, retro_amel_217,
Bos taurus	ENSBTAG00000002953	2 retrocopies	retro_btau_1267, retro_btau_418,
Choloepus hoffmanni	ENSCHOG00000011506	10 retrocopies	retro_chof_1111, retro_chof_127, retro_chof_1557, retro_chof_1680, retro_chof_1696, retro_chof_240, retro_chof_2424, retro_chof_317, retro_chof_617, retro_chof_82,
Callithrix jacchus	ENSCJAG00000017321	5 retrocopies	retro_cjac_1407, retro_cjac_2536, retro_cjac_2733, retro_cjac_3010, retro_cjac_69,
Cavia porcellus	ENSCPOG00000015348	5 retrocopies	retro_cpor_1048, retro_cpor_49, retro_cpor_54, retro_cpor_55, retro_cpor_74,
Dasypus novemcinctus	ENSDNOG00000019205	20 retrocopies	retro_dnov_100, retro_dnov_1047, retro_dnov_1122, retro_dnov_1222, retro_dnov_1353, retro_dnov_1403, retro_dnov_1404, retro_dnov_1628, retro_dnov_1634, retro_dnov_1646, retro_dnov_1949, retro_dnov_1996, retro_dnov_2069, retro_dnov_2197, retro_dnov_2239, retro_dnov_290, retro_dnov_466, retro_dnov_593, retro_dnov_843, retro_dnov_852,
Equus caballus	ENSECAG00000013324	1 retrocopy	retro_ecab_51,
Echinops telfairi	ENSETEG00000003065	13 retrocopies	retro_etel_1173, retro_etel_1256, retro_etel_1672, retro_etel_1725, retro_etel_1807, retro_etel_1831, retro_etel_1932, retro_etel_1956, retro_etel_320, retro_etel_389, retro_etel_737, retro_etel_903, retro_etel_926,
Felis catus	ENSFCAG00000004790	4 retrocopies	retro_fcat_1096, retro_fcat_1105, retro_fcat_2025, retro_fcat_877,
Homo sapiens	ENSG00000136810	7 retrocopies	retro_hsap_1713, retro_hsap_206, retro_hsap_2330, retro_hsap_3052, retro_hsap_3614, retro_hsap_405, retro_hsap_736,
Gorilla gorilla	ENSGGOG00000006925	6 retrocopies	retro_ggor_1283, retro_ggor_1769, retro_ggor_2440, retro_ggor_35, retro_ggor_401, retro_ggor_620,
Loxodonta africana	ENSLAFG00000012856	2 retrocopies	retro_lafr_372, retro_lafr_93,
Macropus eugenii	ENSMEUG00000003515	8 retrocopies	retro_meug_1198, retro_meug_1204, retro_meug_1603, retro_meug_192, retro_meug_2170, retro_meug_2175, retro_meug_539, retro_meug_840,
Microcebus murinus	ENSMICG00000002128	2 retrocopies	retro_mmur_118, retro_mmur_717,
Myotis lucifugus	ENSMLUG00000009065	3 retrocopies	retro_mluc_1268, retro_mluc_1940, retro_mluc_776,
Macaca mulatta	ENSMMUG00000010322	1 retrocopy	retro_mmul_167,
Mustela putorius furo	ENSMPUG00000007426	3 retrocopies	retro_mputfur_1230, retro_mputfur_693, retro_mputfur_840,
Mus musculus	ENSMUSG00000028367	2 retrocopies	retro_mmus_3063, retro_mmus_432,
Otolemur garnettii	ENSOGAG00000009165	6 retrocopies	retro_ogar_1573, retro_ogar_2763, retro_ogar_3141, retro_ogar_3205, retro_ogar_727, retro_ogar_851,
Ochotona princeps	ENSOPRG00000013805	11 retrocopies	retro_opri_1132, retro_opri_1172, retro_opri_220, retro_opri_309, retro_opri_468, retro_opri_643, retro_opri_681, retro_opri_738, retro_opri_81, retro_opri_887, retro_opri_89,
Procavia capensis	ENSPCAG00000014011	1 retrocopy	retro_pcap_311,
Pongo abelii	ENSPPYG00000019491	2 retrocopies	retro_pabe_1428, retro_pabe_2965 ,
Pan troglodytes	ENSPTRG00000021245	7 retrocopies	retro_ptro_1158, retro_ptro_1703, retro_ptro_1988, retro_ptro_2444, retro_ptro_309, retro_ptro_339, retro_ptro_524,
Pteropus vampyrus	ENSPVAG00000007265	1 retrocopy	retro_pvam_433,
Rattus norvegicus	ENSRNOG00000012081	1 retrocopy	retro_rnor_616,
Sorex araneus	ENSSARG00000007465	2 retrocopies	retro_sara_373, retro_sara_525,
Sarcophilus harrisii	ENSSHAG00000006739	1 retrocopy	retro_shar_329,
Sus scrofa	ENSSSCG00000005453	1 retrocopy	retro_sscr_786,
Ictidomys tridecemlineatus	ENSSTOG00000020668	4 retrocopies	retro_itri_6, retro_itri_714, retro_itri_823, retro_itri_884,
Tupaia belangeri	ENSTBEG00000011193	2 retrocopies	retro_tbel_1293, retro_tbel_3405,
Tursiops truncatus	ENSTTRG00000000119	1 retrocopy	retro_ttru_1378,