RetrogeneDB ID: retro_pabe_3127

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:27435319..27435745(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSRB2
• Ensembl ID: ENSPPYG00000002148
• Aliases: None
• Description: methionine sulfoxide reductase B2 [Source:HGNC Symbol;Acc:17061]

Sequence

>retro_pabe_3127
TCTCTTGCAACATGTGAGCTGCCTCTTGCCAAGAGTGAGTAGCAAAAGAAACTAAGCCCAGAGCAGTTCTGTGTCGTGAG
AGAAAAGGGAAGAGAACCACCTTTCAGTGGGATCTACCTGAATAACAAGGAAGCAGGAATGTGTCATTGTGTGTGCTGCA
ATAGTCCACTCTTCAGTTCTGAGAAAAAGTACTGCTCTGGCACTGGGTGGCCTTCATTTTCTGAGGCTCATGGTACGTGT
GGCTCTGATGAAAGCCACACAGGGATCCTGAGACGTCTGGACACCTCGTTAGGATCAGCTCACACAGAGGTCGTCTGCAA
GCAGTGTGAAGCTCATCCTGGTCACGTGGTTCCTGATGGACCCGGGCCCAATGGTCAGAGGTTTTGCATCAACAGTGTGG
CTCTGAAGATCACACCAAGGAAACAT

Alignment

ORF - retro_pabe_3127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 96.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLGTCELPLAKSEWQKKLTPEQFYVTREKGTEPPFSGIYLNNKEAGMYHCVCCDSPLFSSEKKYCSGTGW
          SL.TCELPLAKSE.QKKL.PEQF.V.REKG.EPPFSGIYLNNKEAGM.HCVCC.SPLFSSEKKYCSGTGW
Retrocopy SLATCELPLAKSE*QKKLSPEQFCVVREKGREPPFSGIYLNNKEAGMCHCVCCNSPLFSSEKKYCSGTGW

Parental  PSFSEAHGTSGSDESHTGILRRLDTSLGSARTEVVCKQCEAHLGHVFPDGPGPNGQRFCINSVALKFKPR
          PSFSEAHGT.GSDESHTGILRRLDTSLGSA.TEVVCKQCEAH.GHV.PDGPGPNGQRFCINSVALK..PR
Retrocopy PSFSEAHGTCGSDESHTGILRRLDTSLGSAHTEVVCKQCEAHPGHVVPDGPGPNGQRFCINSVALKITPR

Parental  KH
          KH
Retrocopy KH

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	18.69 RPM
SRP007412_cerebellum	0.00 RPM	16.05 RPM
SRP007412_heart	0.00 RPM	23.99 RPM
SRP007412_kidney	0.03 RPM	24.16 RPM
SRP007412_liver	0.03 RPM	50.03 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3127 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3127 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3127 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006388	1 retrocopy	retro_amel_505,
Canis familiaris	ENSCAFG00000004215	1 retrocopy	retro_cfam_1147,
Equus caballus	ENSECAG00000013072	1 retrocopy	retro_ecab_593,
Nomascus leucogenys	ENSNLEG00000012892	1 retrocopy	retro_nleu_2871,
Pongo abelii	ENSPPYG00000002148	1 retrocopy	retro_pabe_3127 ,
Sus scrofa	ENSSSCG00000011077	1 retrocopy	retro_sscr_218,