RetrogeneDB ID: retro_pabe_92

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:40700249..40701317(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000012328
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000004581
• Aliases: None
• Description: None

Sequence

>retro_pabe_92
ATGGATGCCGGTGTGACTGAAAGTGGACTAAATGTGACTCTCACCATTCGGCTTCTTATGCACGGAAAGGAAGTAGGAAG
CATCATTGGGAAGAAAGGGGAGTCGGTTAAGAGGATCCGCGAGGAGAGTGGCGCGCGGATCAACATCTCGGAGGGGAATT
GTCCTGAGAGAATCATCACTCTGACCGGCCCCACCAATGCCATCTTTAAGGCTTTCGCTATGATCATCGACAAGCTGGAG
GAAGATATCAACAGCTCCATGACCAACAGCACCGCGGCCAGCAGGCCCCCGGTCACCCTGAGGCTGGTGGTGCCGGCCAC
CCAGTGCGGCTCCCTGATTGGGAAAGGCGGGTGTAAGATCAAAGAGATCCGCGAGAGTACGGGGGCGCAGGTCCAGGTGG
CGGGGGATATGCTGCCCAACTCCACCGAGCGGGCCATCACCATCGCTGGCGTGCCGCAGTCTGTCACCGAGTGTGTCAAG
CAGATCTGCCTGGTCATGCTGGAGACGCTCTCCCAGTCTCCGCAAGGAAGAGTCATGACCATTCCGTACCAGCCCATGCC
GGCCAGCTCCCCAGTCATCTGCGCGGGCGGCCAAGATCGGTGCAGCGACGCTGCGGGCTACCCCCATGCCACCCATGACC
TGGAGGGACCACCTCTAGATGCCTACTCGATTCAAGGACAACACACCATTTCTCCGCTCGATCTGGCCAAGCTGAACCAG
GTGGCAAGACAACAGTCTCACTTTGCCATGATGCACGGCGGGACCGGATTCGCCGGAATTGACTCCAGCTCTCCAGAGGT
GAAAGGCTATTGGGCAAGTTTGGATGCATCTACTCAAACCACCCATGAACTCACCATTCCAAATAACTTAATTGGCTGCA
TAATCGGGCGCCAAGGCGCCAACATTAATGAGATCCGCCAGATGTCCGGGGCCCAGATCAAAATTGCCAACCCAGTGGAA
GGCTCCTCTGGTAGGCAGGTTACTATCACTGGCTCTGCTGCCAGTATTAGTCTGGCCCAGTATCTAATCAATGCCAGGCT
TTCCTCTGAGAAGGGCATGGGGTGCAGC

Alignment

ORF - retro_pabe_92 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.58 %
• Parental protein coverage: 57.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
          MD.GV.E.GLNVTLTIRLLMHGKEVGSIIGKKGESVK..REESGARINISEGNCPERIITL.GPTNAIFK
Retrocopy MDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFK

Parental  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
          AFAMIIDKLEEDI.SSMTNSTAASRPPVTLRLVVPA.QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
Retrocopy AFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN

Parental  STERAITIAGIPQSIIECVKQICVVMLES---PPKG--VTIPYRPKPSSSPVIFAGGQDRYSTGSDSASF
          STERAITIAG.PQS..ECVKQIC.VMLE.....P.G...TIPY.P.P.SSPVI.AGGQDR.S...D.A..
Retrocopy STERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDRCS---DAAGY

Parental  PHTT
          PH.T
Retrocopy PHAT

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	119.43 RPM	142.87 RPM
SRP007412_cerebellum	68.95 RPM	187.51 RPM
SRP007412_heart	56.08 RPM	89.08 RPM
SRP007412_kidney	157.08 RPM	230.47 RPM
SRP007412_liver	146.70 RPM	136.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_92 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_92 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_92 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_175
Sus scrofa	retro_sscr_61
Equus caballus	retro_ecab_67
Oryctolagus cuniculus	retro_ocun_10

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020757	1 retrocopy	retro_btau_175,
Canis familiaris	ENSCAFG00000006821	1 retrocopy	retro_cfam_54,
Callithrix jacchus	ENSCJAG00000018590	2 retrocopies	retro_cjac_3253, retro_cjac_754,
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Dasypus novemcinctus	ENSDNOG00000008688	6 retrocopies	retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Echinops telfairi	ENSETEG00000014741	3 retrocopies	retro_etel_1170, retro_etel_2108, retro_etel_840,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Gorilla gorilla	ENSGGOG00000012613	2 retrocopies	retro_ggor_212, retro_ggor_2734,
Macropus eugenii	ENSMEUG00000001887	7 retrocopies	retro_meug_1143, retro_meug_1988, retro_meug_432, retro_meug_526, retro_meug_618, retro_meug_828, retro_meug_964,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus	ENSMLUG00000009971	3 retrocopies	retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Mus musculus	ENSMUSG00000056851	1 retrocopy	retro_mmus_274,
Nomascus leucogenys	ENSNLEG00000017693	1 retrocopy	retro_nleu_10,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,
Pongo abelii	ENSPPYG00000004581	2 retrocopies	retro_pabe_3346, retro_pabe_92 ,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Pan troglodytes	ENSPTRG00000005018	1 retrocopy	retro_ptro_113,
Pteropus vampyrus	ENSPVAG00000012284	3 retrocopies	retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus	ENSRNOG00000036852	2 retrocopies	retro_rnor_1238, retro_rnor_2088,
Sus scrofa	ENSSSCG00000000274	1 retrocopy	retro_sscr_61,
Ictidomys tridecemlineatus	ENSSTOG00000003635	2 retrocopies	retro_itri_1522, retro_itri_557,
Vicugna pacos	ENSVPAG00000000406	1 retrocopy	retro_vpac_471,