RetrogeneDB ID: retro_pabe_3083

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:102328259..102328718(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF181
• Ensembl ID: ENSPPYG00000012225
• Aliases: None
• Description: ring finger protein 181 [Source:HGNC Symbol;Acc:28037]

Sequence

>retro_pabe_3083
ATGGCGTCCTATATCGATGAACACGACTGTGAGCCGTTGGACCCTCAAGCAGGAGACTCGAACCAATATGGTGCTGGAGC
TCGTAAGGTCACTTTTCAATAGGATGGACTTTGAAGACTTGGGGTTGGTAGTAGATTGGGACCACCACCTGCCTCCACCA
GCTGCCAAGATTGTGGTTGAGAACCTCCCCAGGACAGTCATCAGAGGCTTTCAGGATGAGCTCAAGTGCCTCGTGTGTCT
TTTGGAATCTGAGGAGGAGGAGACTGCCATCGAGATGCTTCCCATCACCTTTTCCATTCCAGCTGCATTCTGCCCTGGCT
AAGCAAGACAAATTCCTGTCCCTTGTGCCGCCATGAGCTGCCCACTGATGACTACACTTATGAGGAGCACAGACGAGATA
AGGCTCGAAAACAGCAGCAGCAGAACCTACTGGAGAACCTCCATGGAGCCATGTACACG

Alignment

ORF - retro_pabe_3083 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASYFDEHDCEPSDPE-QETRTNMLLELARSLFNRMDFEDLGLVVDWDHHLPPPAAKTVVENLPRTVIRG
          MASY.DEHDCEP.DP..QETRTNM.LEL.RSLFNRMDFEDLGLVVDWDHHLPPPAAK.VVENLPRTVIRG
Retrocopy MASYIDEHDCEPLDPQ>QETRTNMVLELVRSLFNRMDFEDLGLVVDWDHHLPPPAAKIVVENLPRTVIRG

Parental  SQAELKCPVCLLEFEEEETAIEM-PCHHLFHSSCILPWLSKTNSCPLCRHELPTDDDTYEEHRRDKARKQ
          .Q.ELKC.VCLLE.EEEETAIEM...HHLFHSSCILPWLSKTNSCPLCRHELPTDD.TYEEHRRDKARKQ
Retrocopy FQDELKCLVCLLESEEEETAIEM<ASHHLFHSSCILPWLSKTNSCPLCRHELPTDDYTYEEHRRDKARKQ

Parental  QQQHRLENLHGAMYT
          QQQ..LENLHGAMYT
Retrocopy QQQNLLENLHGAMYT

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	1.38 RPM
SRP007412_cerebellum	0.00 RPM	0.97 RPM
SRP007412_heart	0.00 RPM	0.87 RPM
SRP007412_kidney	0.03 RPM	1.82 RPM
SRP007412_liver	0.03 RPM	1.44 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3083 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3083 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3083 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3771
Pan troglodytes	retro_ptro_2557
Gorilla gorilla	retro_ggor_2537
Macaca mulatta	retro_mmul_1637

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019647	3 retrocopies	retro_cjac_2423, retro_cjac_355, retro_cjac_3849,
Homo sapiens	ENSG00000168894	3 retrocopies	retro_hsap_1005, retro_hsap_3771, retro_hsap_938,
Gorilla gorilla	ENSGGOG00000004953	3 retrocopies	retro_ggor_2537, retro_ggor_759, retro_ggor_799,
Macaca mulatta	ENSMMUG00000017824	3 retrocopies	retro_mmul_1128, retro_mmul_1637, retro_mmul_808,
Otolemur garnettii	ENSOGAG00000012284	1 retrocopy	retro_ogar_2742,
Pongo abelii	ENSPPYG00000012225	2 retrocopies	retro_pabe_3083 , retro_pabe_807,
Pan troglodytes	ENSPTRG00000012138	2 retrocopies	retro_ptro_2557, retro_ptro_650,