RetrogeneDB ID: retro_pabe_1956

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:55589643..55590125(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000029576
• Aliases: None
• Description: None

Sequence

>retro_pabe_1956
ATGAAAGAAGCAATCATGAACCAGGGAAAACTCACAAATTGCAGGCACAAGCGCGCATTGGTGGGAAAGGAACTGCTTGC
CGAAAGAAGGTGGTTCACAGAGCAGCTGCAGCAGATGATAAAAAACTTCAGTTCTCCTTAAAGAAGTTAGGGGTAAACAA
TATCTCTGGTATTGAAGAGGTGAATACATTTACAAACTAAGGAACAGTAACCACTTTAACAACCCTAAAGTTCAGGCATC
TCTGGCAGCGAACACTTTTCACCATTACAGGCCATGCTGAGATAAAGCAGCTGACAGAAATGCTACCCAGCATCTTAAAC
CAGCTTGGTGCAGGCAGTCTGACTAGTATAAGGAGACTGGCTGAAGCTCTGCCCAAACAATCTGTGGATGGAAAAGTACC
ACTTGCTACTGGACAGGATGATGATGATGAAGTTCCAGATCTTGTGGAGAAATTCGAAGAGGCTTCCAAGAATGGGGCAA
AC

Alignment

ORF - retro_pabe_1956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKETIMNQEKLA-KLQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLGVNNISGIEEVNMFTNQG
          MKE.IMNQ.KL..KLQAQ.RIGGKGTA.RKK.VVHR.A.ADDKKLQFSLKKLGVNNISGIEEVN.FTN.G
Retrocopy MKEAIMNQGKLT<KLQAQARIGGKGTACRKK-VVHRAAAADDKKLQFSLKKLGVNNISGIEEVNTFTN*G

Parental  TVI-HFNNPKVQASLAANT-FTITGHAETKQLTEMLPSILNQLGADSLTSLRRLAEALPKQSVDGKAPLA
          TV..HFNNPKVQASLAANT.FTITGHAE.KQLTEMLPSILNQLGA.SLTS.RRLAEALPKQSVDGK.PLA
Retrocopy TVT<HFNNPKVQASLAANT>FTITGHAEIKQLTEMLPSILNQLGAGSLTSIRRLAEALPKQSVDGKVPLA

Parental  TGEDDDDEVPDLVENFDEASKNEAN
          TG.DDDDEVPDLVE.F.EASKN.AN
Retrocopy TGQDDDDEVPDLVEKFEEASKNGAN

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	34.17 RPM
SRP007412_cerebellum	0.00 RPM	40.37 RPM
SRP007412_heart	0.00 RPM	49.76 RPM
SRP007412_kidney	0.03 RPM	63.01 RPM
SRP007412_liver	0.00 RPM	69.01 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1956 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1956 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1956 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2259
Pan troglodytes	retro_ptro_1599
Gorilla gorilla	retro_ggor_1682

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010012	5 retrocopies	retro_btau_1161, retro_btau_1344, retro_btau_1361, retro_btau_459, retro_btau_551,
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Equus caballus	ENSECAG00000021629	1 retrocopy	retro_ecab_200,
Echinops telfairi	ENSETEG00000017341	5 retrocopies	retro_etel_1216, retro_etel_1394, retro_etel_1997, retro_etel_405, retro_etel_960,
Gorilla gorilla	ENSGGOG00000000166	10 retrocopies	retro_ggor_1082, retro_ggor_1682, retro_ggor_1961, retro_ggor_2054, retro_ggor_2399, retro_ggor_2647, retro_ggor_2667, retro_ggor_548, retro_ggor_81, retro_ggor_946,
Microcebus murinus	ENSMICG00000017182	3 retrocopies	retro_mmur_1219, retro_mmur_1301, retro_mmur_651,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Nomascus leucogenys	ENSNLEG00000004718	9 retrocopies	retro_nleu_1081, retro_nleu_1199, retro_nleu_1284, retro_nleu_1446, retro_nleu_1797, retro_nleu_2526, retro_nleu_451, retro_nleu_496, retro_nleu_734,
Oryctolagus cuniculus	ENSOCUG00000024914	6 retrocopies	retro_ocun_1186, retro_ocun_1299, retro_ocun_1364, retro_ocun_446, retro_ocun_857, retro_ocun_916,
Pongo abelii	ENSPPYG00000001353	2 retrocopies	retro_pabe_1850, retro_pabe_3010,
Pongo abelii	ENSPPYG00000029576	14 retrocopies	retro_pabe_1154, retro_pabe_1477, retro_pabe_180, retro_pabe_1885, retro_pabe_1956 , retro_pabe_2207, retro_pabe_2458, retro_pabe_2918, retro_pabe_2919, retro_pabe_2932, retro_pabe_3329, retro_pabe_3484, retro_pabe_558, retro_pabe_649,
Rattus norvegicus	ENSRNOG00000016912	9 retrocopies	retro_rnor_187, retro_rnor_194, retro_rnor_2121, retro_rnor_2520, retro_rnor_2990, retro_rnor_2991, retro_rnor_2999, retro_rnor_836, retro_rnor_953,