RetrogeneDB ID: retro_pabe_3062

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:53874610..53874985(+)
• Located in intron of: ENSPPYG00000017678

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000025906
• Aliases: None
• Description: None

Sequence

>retro_pabe_3062
ATGAAACTGCTCACCCACAATTTGCTGAGCTCGCATGTGCGGGGGGTGGGGTCCCGTGGCTTCCCCCTGCGCCTCCAGGC
CACCGAGGTCCGTATCTGCCCCGTGGAATTCAACCCCAACTTCGTGGCGTGTATGATACCTAAAGTGGAGTGGTCGGCGT
TCCTGGAGGCAGCCGATAACTTGCGCCTGATCCAGGTGCCTAAAGGGCCGGTTGAGGGATATGAGGAGAATGAGGAATTT
CTGAGGACCATGCACCACCTGCTGCTGGAGGTGGAAGTGACAGAGGGCACCCTGCAGTGCCCAGAATCTGGATGTATGTT
CCCCATCAGCCGCGGGATCCCCAACATGCTGCTGAGTGAAGAGGAGACTGAGAGT

Alignment

ORF - retro_pabe_3062 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLLTHNLLSSHVRGVGSRGFPLRLQATEVRICPVEFNPNFVARMIPKVEWSAFLEAADNLRLIQVPKGP
          MKLLTHNLLSSHVRGVGSRGFPLRLQATEVRICPVEFNPNFVA.MIPKVEWSAFLEAADNLRLIQVPKGP
Retrocopy MKLLTHNLLSSHVRGVGSRGFPLRLQATEVRICPVEFNPNFVACMIPKVEWSAFLEAADNLRLIQVPKGP

Parental  VEGYEENEEFLRTMHHLLLEVEVIEGTLQCPESGRMFPISRGIPNMLLSEEETES
          VEGYEENEEFLRTMHHLLLEVEV.EGTLQCPESG.MFPISRGIPNMLLSEEETES
Retrocopy VEGYEENEEFLRTMHHLLLEVEVTEGTLQCPESGCMFPISRGIPNMLLSEEETES

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	50.04 RPM
SRP007412_cerebellum	0.00 RPM	25.66 RPM
SRP007412_heart	0.27 RPM	12.22 RPM
SRP007412_kidney	0.03 RPM	66.29 RPM
SRP007412_liver	0.24 RPM	39.29 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3062 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3062 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3062 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017965	3 retrocopies	retro_amel_125, retro_amel_1748, retro_amel_295,
Bos taurus	ENSBTAG00000008646	1 retrocopy	retro_btau_410,
Callithrix jacchus	ENSCJAG00000018026	1 retrocopy	retro_cjac_2995,
Equus caballus	ENSECAG00000016960	1 retrocopy	retro_ecab_103,
Homo sapiens	ENSG00000173113	4 retrocopies	retro_hsap_1853, retro_hsap_2847, retro_hsap_2974, retro_hsap_86,
Gorilla gorilla	ENSGGOG00000001334	3 retrocopies	retro_ggor_1669, retro_ggor_2157, retro_ggor_2867,
Macaca mulatta	ENSMMUG00000019647	2 retrocopies	retro_mmul_1267, retro_mmul_2181,
Nomascus leucogenys	ENSNLEG00000004991	4 retrocopies	retro_nleu_1599, retro_nleu_2137, retro_nleu_2169, retro_nleu_556,
Pongo abelii	ENSPPYG00000025906	5 retrocopies	retro_pabe_1510, retro_pabe_2357, retro_pabe_3062 , retro_pabe_3332, retro_pabe_3496,
Pteropus vampyrus	ENSPVAG00000017134	1 retrocopy	retro_pvam_853,
Ictidomys tridecemlineatus	ENSSTOG00000019857	1 retrocopy	retro_itri_208,