RetrogeneDB ID: retro_pabe_360

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:9321024..9321597(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000025872
• Aliases: None
• Description: None

Sequence

>retro_pabe_360
TCCAGCACCAGGATCATGAAGCCCAAGAGCGAGAAGCCAGGCGAGTTCAAGTCCGGTATCTCCCAGGCTCTTCTGGAGCT
GGAGATTAACTCGGACCTCAAGGCTCAGTTCAGGGAGCTGAATATTACAGCAGCCAAGGAAACTGAAGATGGTGGTGGTG
GGAAAAGCTATCATAATTTTTGTTCCCATTCCTCAACTGAAATCTTTCCAGAAAATCCAAGTCTGGCTAGTACGTGAATT
GGAGAAAAAGTTTGGGGGAAGCATGTTGTCTTTATTGCTCAGAGGAGAATTCTGCCTAAGCCAACCTGAAAAAGCTGTAC
AAAAAAGAAGCAAAGGCGTCCCAGGAGCCGTACCCTGAAAGCCATGCATGACTCAGTCCCCGAGGACTTGGTCTTCCCAA
GTGTAATTGTGGGCAAGAGAATCCACGTGAAACTGGATGGCAGCCGTCTCATAAAGGCTCATTTGGACAAAGTGCAGCAA
AACAATGTGGAACGCAACGTTGAAACTTTTTCTGGTGTCTATATGAAGCTCACAGGCAAGGATATAAATTTTGAATTCCC
AGAGTTTCAACTC

Alignment

ORF - retro_pabe_360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.38 %
• Parental protein coverage: 98.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRK-AIIIFVPVPQLKSF
          SS..I.KP..EKP.EF.SGISQALLELE.NSDLKAQ.RELNITAAKE.E.GGG.K.AIIIFVP.PQLKSF
Retrocopy SSTRIMKPKSEKPGEFKSGISQALLELEINSDLKAQFRELNITAAKETEDGGGGK>AIIIFVPIPQLKSF

Parental  QKIQVRLVRELEKKFS-GKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVG
          QKIQV.LVRELEKKF..GKHVVFIAQRRILPKPT.KS.TK.KQ.RPRSRTL.A.HD...EDLVFPS.IVG
Retrocopy QKIQVWLVRELEKKFG<GKHVVFIAQRRILPKPT*KSCTKKKQRRPRSRTLKAMHDSVPEDLVFPSVIVG

Parental  KRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL
          KRI.VKLDGSRLIK.HLDK.QQNNVE..VETFSGVY.KLTGKD.NFEFPEFQL
Retrocopy KRIHVKLDGSRLIKAHLDKVQQNNVERNVETFSGVYMKLTGKDINFEFPEFQL

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	0.06 RPM	28.03 RPM
SRP007412_cerebellum	0.00 RPM	39.52 RPM
SRP007412_heart	0.00 RPM	36.49 RPM
SRP007412_kidney	0.00 RPM	59.47 RPM
SRP007412_liver	0.00 RPM	62.52 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_360 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_360 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_329

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 120 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016224	5 retrocopies	retro_btau_1016, retro_btau_1046, retro_btau_1351, retro_btau_448, retro_btau_997,
Canis familiaris	ENSCAFG00000003263	1 retrocopy	retro_cfam_1798,
Callithrix jacchus	ENSCJAG00000016462	2 retrocopies	retro_cjac_16, retro_cjac_2287,
Cavia porcellus	ENSCPOG00000009795	2 retrocopies	retro_cpor_1139, retro_cpor_773,
Dasypus novemcinctus	ENSDNOG00000013285	14 retrocopies	retro_dnov_1091, retro_dnov_1351, retro_dnov_1388, retro_dnov_1459, retro_dnov_1688, retro_dnov_1849, retro_dnov_1940, retro_dnov_1970, retro_dnov_238, retro_dnov_2409, retro_dnov_558, retro_dnov_582, retro_dnov_623, retro_dnov_791,
Equus caballus	ENSECAG00000020253	2 retrocopies	retro_ecab_276, retro_ecab_396,
Felis catus	ENSFCAG00000023243	2 retrocopies	retro_fcat_1534, retro_fcat_41,
Homo sapiens	ENSG00000171863	14 retrocopies	retro_hsap_111, retro_hsap_112, retro_hsap_1242, retro_hsap_1737, retro_hsap_1837, retro_hsap_2907, retro_hsap_2925, retro_hsap_329, retro_hsap_3635, retro_hsap_404, retro_hsap_4711, retro_hsap_4760, retro_hsap_528, retro_hsap_703,
Gorilla gorilla	ENSGGOG00000023095	13 retrocopies	retro_ggor_2028, retro_ggor_2090, retro_ggor_2161, retro_ggor_218, retro_ggor_2452, retro_ggor_2927, retro_ggor_294, retro_ggor_2965, retro_ggor_3047, retro_ggor_346, retro_ggor_400, retro_ggor_484, retro_ggor_597,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Monodelphis domestica	ENSMODG00000014495	2 retrocopies	retro_mdom_662, retro_mdom_810,
Mus musculus	ENSMUSG00000061477	2 retrocopies	retro_mmus_271, retro_mmus_53,
Nomascus leucogenys	ENSNLEG00000015407	10 retrocopies	retro_nleu_1505, retro_nleu_1771, retro_nleu_1783, retro_nleu_2278, retro_nleu_2346, retro_nleu_2510, retro_nleu_2892, retro_nleu_3080, retro_nleu_817, retro_nleu_835,
Oryctolagus cuniculus	ENSOCUG00000008507	2 retrocopies	retro_ocun_203, retro_ocun_230,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Ochotona princeps	ENSOPRG00000005085	3 retrocopies	retro_opri_1036, retro_opri_415, retro_opri_500,
Pongo abelii	ENSPPYG00000025872	12 retrocopies	retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360 , retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Pan troglodytes	ENSPTRG00000011615	3 retrocopies	retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Pteropus vampyrus	ENSPVAG00000002071	7 retrocopies	retro_pvam_1051, retro_pvam_1183, retro_pvam_1330, retro_pvam_1437, retro_pvam_207, retro_pvam_543, retro_pvam_887,
Rattus norvegicus	ENSRNOG00000008551	2 retrocopies	retro_rnor_39, retro_rnor_391,
Ictidomys tridecemlineatus	ENSSTOG00000024830	3 retrocopies	retro_itri_1147, retro_itri_1161, retro_itri_1215,
Tursiops truncatus	ENSTTRG00000001616	6 retrocopies	retro_ttru_1422, retro_ttru_1659, retro_ttru_1706, retro_ttru_301, retro_ttru_323, retro_ttru_773,