RetrogeneDB ID: retro_pabe_1923

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:8191789..8192136(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000006487
• Aliases: None
• Description: None

Sequence

>retro_pabe_1923
AGAGGGAGCACTATGTCTGTGGAAGTCTCCGAGGCAGCCTCTGTGGAGGAGCAGAAGGAAATGAAGATACAGTGACTAGT
TCAGAGAAAGCTGAAGAAGCAAAATTAAAAGCAAGATATCCTCATCTGGGACAAATGCCTGGAGGTTCAGATTTCTTAAG
GAAACGATTGCAGAAAAGGCAAAAATATTTTGATTCTGGGGATTACAACATGGCTAAAGCAAAAATGAAGAACGAGCAAC
TTCCTACTGCAGCTCTGGATAAGACGGAGGTCACGGGTGACCACATTCCCACTCCAGAGGACCTTCCTCAATGGAAACCA
TCCATTGTTGCCAGCAAGCTGGCTGGT

Alignment

ORF - retro_pabe_1923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 96.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KGSTMSAEVPEAASAEEQKEM-EDKVTSPEKAEEAKLKARYPHLGQKPGGSDFLRKRLQKGQKYFDSGDY
          .GSTMS.EV.EAAS.EEQKEM.ED.VTS.EKAEEAKLKARYPHLGQ.PGGSDFLRKRLQK.QKYFDSGDY
Retrocopy RGSTMSVEVSEAASVEEQKEM<EDTVTSSEKAEEAKLKARYPHLGQMPGGSDFLRKRLQKRQKYFDSGDY

Parental  NMAKAKMKNKQLPTAAPDKTEVTGDHIPTPQDLPQRKPSLVASKLAG
          NMAKAKMKN.QLPTAA.DKTEVTGDHIPTP.DLPQ.KPS.VASKLAG
Retrocopy NMAKAKMKNEQLPTAALDKTEVTGDHIPTPEDLPQWKPSIVASKLAG

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	52.91 RPM
SRP007412_cerebellum	0.00 RPM	14.71 RPM
SRP007412_heart	0.00 RPM	7.86 RPM
SRP007412_kidney	0.00 RPM	8.78 RPM
SRP007412_liver	0.00 RPM	4.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1923 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1923 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011022	5 retrocopies	retro_btau_1259, retro_btau_1821, retro_btau_1845, retro_btau_952, retro_btau_981,
Canis familiaris	ENSCAFG00000032515	2 retrocopies	retro_cfam_1375, retro_cfam_1402,
Cavia porcellus	ENSCPOG00000011228	1 retrocopy	retro_cpor_1148,
Dasypus novemcinctus	ENSDNOG00000004474	9 retrocopies	retro_dnov_1086, retro_dnov_1576, retro_dnov_1960, retro_dnov_2150, retro_dnov_2427, retro_dnov_557, retro_dnov_616, retro_dnov_644, retro_dnov_662,
Dipodomys ordii	ENSDORG00000011321	2 retrocopies	retro_dord_194, retro_dord_33,
Echinops telfairi	ENSETEG00000015550	1 retrocopy	retro_etel_585,
Homo sapiens	ENSG00000128989	2 retrocopies	retro_hsap_2130, retro_hsap_3280,
Gorilla gorilla	ENSGGOG00000025250	1 retrocopy	retro_ggor_198,
Loxodonta africana	ENSLAFG00000000755	2 retrocopies	retro_lafr_1058, retro_lafr_574,
Macaca mulatta	ENSMMUG00000008344	1 retrocopy	retro_mmul_1001,
Nomascus leucogenys	ENSNLEG00000006551	2 retrocopies	retro_nleu_2533, retro_nleu_2884,
Oryctolagus cuniculus	ENSOCUG00000015489	10 retrocopies	retro_ocun_1182, retro_ocun_1297, retro_ocun_1398, retro_ocun_1573, retro_ocun_1731, retro_ocun_1768, retro_ocun_310, retro_ocun_473, retro_ocun_479, retro_ocun_698,
Otolemur garnettii	ENSOGAG00000013865	1 retrocopy	retro_ogar_591,
Pongo abelii	ENSPPYG00000000893	2 retrocopies	retro_pabe_1803, retro_pabe_2081,
Pongo abelii	ENSPPYG00000006487	2 retrocopies	retro_pabe_120, retro_pabe_1923 ,
Pan troglodytes	ENSPTRG00000042183	1 retrocopy	retro_ptro_1559,
Pteropus vampyrus	ENSPVAG00000004012	1 retrocopy	retro_pvam_205,
Sus scrofa	ENSSSCG00000004618	1 retrocopy	retro_sscr_603,
Ictidomys tridecemlineatus	ENSSTOG00000003677	7 retrocopies	retro_itri_1075, retro_itri_1290, retro_itri_1339, retro_itri_1643, retro_itri_1657, retro_itri_1865, retro_itri_594,
Tursiops truncatus	ENSTTRG00000004804	1 retrocopy	retro_ttru_172,