RetrogeneDB ID: retro_pabe_2233

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:100683918..100684393(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHD
• Ensembl ID: ENSPPYG00000003876
• Aliases: None
• Description: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5RC29]

Sequence

>retro_pabe_2233
ATGGAGGTTCTCTAGAGGCTGAGTGCCCTCTGTGGTGCCCAGGGAGGCTGAGCTCTGTTCCTGCGAGCCCCAGTTGTTAG
ACCTGCTCAGATCTCAGGATTTCTTCAGGACCCAACCTACCCCAGAATGGCGTGGAGTGCAGCACATTCATTTGTCACTG
AGCCACCTTTCTGGTTCCAAGCCTGCGTCTTTCCACTGGGACTAGTGAGAGGATTGTCAGTGTTTTGCTCTTGGGCCTGC
TTCCAGCTGCTTATCTGAATCCTTGCTCTGTGATGGCCTACTCCGTAGCTGCAACCCTCACTCTTCATGGTCTTGGGGCC
TTGGACAAGTTGTTCCTGACTGTGTTCATGGGGATGCATTGCAGAAAGCTGCCAAGGCAGGCCTTTCGGCACTTTCAGCT
TTAGCCTTTGCTGGGCTTTGCTCTTTCAACTATCATGATGTGGGCATCTGCAAAGATGCTGCCACACTGTGGAAG

Alignment

ORF - retro_pabe_2233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.5 %
• Parental protein coverage: 99.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAVLWRLSAVCGAQGGRALLLRTPVVRPAHISAFLQD-RPIPEWCGVQHIHLSPGHHSGSKAASLHW-TS
          M.VL.RLSA.CGAQGG.AL.LR.PVVRPA.IS.FLQD..P.PEW.GVQHIHLS..H.SGSK.AS.HW.TS
Retrocopy MEVL*RLSALCGAQGG*ALFLRAPVVRPAQISGFLQD>QPTPEWRGVQHIHLSLSHLSGSKPASFHW>TS

Parental  ERVVSVLLLGLLPAAYLNPCSAMDYSLAATLTLHG-HWGLGQVVTDYVHGDASQKAAKAGLLALSALTFA
          ER.VSVLLLGLLPAAYLNPCS.M.YS.AATLTLHG..WGLGQVV.D.VHGDA.QKAAKAGL.ALSAL.FA
Retrocopy ERIVSVLLLGLLPAAYLNPCSVMAYSVAATLTLHG<SWGLGQVVPDCVHGDALQKAAKAGLSALSALAFA

Parental  GLCYFNYHDVGICKAVAMLWK
          GLC.FNYHDVGICK..A.LWK
Retrocopy GLCSFNYHDVGICKDAATLWK

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	8.46 RPM
SRP007412_cerebellum	0.00 RPM	5.23 RPM
SRP007412_heart	0.00 RPM	23.00 RPM
SRP007412_kidney	0.00 RPM	24.73 RPM
SRP007412_liver	0.00 RPM	22.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2233 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2233 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2233 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2784
Callithrix jacchus	retro_cjac_1385

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010975	4 retrocopies	retro_cjac_1385, retro_cjac_1390, retro_cjac_1557, retro_cjac_3829,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355, retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224,
Otolemur garnettii	ENSOGAG00000008568	5 retrocopies	retro_ogar_1651, retro_ogar_1795, retro_ogar_2087, retro_ogar_3122, retro_ogar_3147,
Pongo abelii	ENSPPYG00000003876	5 retrocopies	retro_pabe_1549, retro_pabe_1924, retro_pabe_2233 , retro_pabe_2999, retro_pabe_3096,