RetrogeneDB ID: retro_pabe_2472

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:134850293..134850776(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MBTD1
• Ensembl ID: ENSPPYG00000008267
• Aliases: None
• Description: mbt domain containing 1 [Source:HGNC Symbol;Acc:19866]

Sequence

>retro_pabe_2472
TATGGTGGCTATAGTGAGGACCCAAGTCATAGCTCAGGCTCTGGTGAAAGAAAGTGAGAAATCGCTCCTTTATCTTTTAA
TCTTCTAATTATAAAACATGAATAGACAAACTTTTGCTACACAGATGGCAAATCTGGCAATGCTGCTGGCACTATGCATG
AAATAGTTGGTTTACAGGATGTTTTCTACTCTAAAACAAAATATTCTTGCAGTGTTTCATGTTCAAGAGTGTATTCATCA
AATTCCAAAGAGTTTTGGCCTGACTTCAGATAACAGGTAAGCCGACATCAAAGAAAGCAAGAGTTCCTCAGAAACAGACT
TAGCTGATAAACTGGAAGCATATGCTCAGGATCATGCCACTTTGCAGAATCAAGAGAAGACTAAAGCAGCAGCAGTCTCC
ATGGAAGTTTCAGCTGAGATAACAACATCATTAGCAGTAGTTTTCTGCAGCTTATTACTGGCTTTAAGCGTGCACTCATA
GGA

Alignment

ORF - retro_pabe_2472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.17 %
• Parental protein coverage: 80.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YDSCSEDTSSSSSSEESEEEVAPLPSNLPIIKNNGQVYTYPDGKSGMATCEMCGMVGVRDAFYSKTKRFC
          Y...SED.S.SS.S.E...E.APL..NL.IIK.......Y.DGKSG.A...M...VG..D.FYSKTK..C
Retrocopy YGGYSEDPSHSSGSGERK*EIAPLSFNLLIIKHE*TNFCYTDGKSGNAAGTMHEIVGLQDVFYSKTKYSC

Parental  SVSCSRSYSSNS-KKASILARLQGKPPTKKAKVLQKQP-LVAKLAAYAQYQATLQNQAKTKAGNIAVSME
          SVSCSR.YSSNS...........GKP..KKA.V.QKQ..L..KL.AYAQ..ATLQNQ.KTKA...AVSME
Retrocopy SVSCSRVYSSNS<QRVLA*LQITGKPTSKKARVPQKQT<LADKLEAYAQDHATLQNQEKTKAA--AVSME

Parental  -GFSWGNYINSNSFIAAPVTCFKHAPMG
          ..FS..N.I.S.SF.....T.FK.A..G
Retrocopy <SFS*DNNIISSSFLQL-ITGFKRALIG

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	1.00 RPM
SRP007412_cerebellum	0.00 RPM	3.40 RPM
SRP007412_heart	0.00 RPM	0.72 RPM
SRP007412_kidney	0.00 RPM	1.26 RPM
SRP007412_liver	0.00 RPM	0.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2472 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2472 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007934	1 retrocopy	retro_nleu_128,
Pongo abelii	ENSPPYG00000008267	1 retrocopy	retro_pabe_2472 ,