RetrogeneDB ID: retro_pabe_832

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:32973080..32973749(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM98B
• Ensembl ID: ENSPPYG00000006336
• Aliases: None
• Description: family with sequence similarity 98, member B [Source:HGNC Symbol;Acc:26773]

Sequence

>retro_pabe_832
CTGCTGAAAATTAATTTAAATTTGAAACAGGCAGAACAACTGGAAAGAGTCAATGATGCTCTTTCCTGTGAACATGAGTG
CCTCCAGCGAATGCTATGAAATGATTAGATGCGGCAATACAGTCCGTTGGACGGTGTGATACAGCCAAGGTAAGAACAGA
TGACACAGCAAGAATTTACCAGCCTAAGTGTTATGCTTTGTCACCCAAGACAGCGATTATAATGGTGCATCTACTTGCTG
CTCATGATGATCTATCCAAGATCATTAGGACAAGCAGTGGAGCCAGCCGGAAGATGGCATGTGCCATTAATAAGGTGCTG
ATGGGAAGGGTGCCTGACAGGGAAGGCTGGCCAAATGAAATTGAACCACCACCCTCTGAAATGCCCCCTTGGCAAAGAGA
CAAGAGGGCAGTGGCGGAAGGGGTGGTTGGGGTGGTGGTCGTGGAGATAGAGGTGGTAGTAGAAGAGGCTGTGGGGGTGG
AAGTGGAAGAGGTGGCTGGCGTGGAGGAGGATGGGAAAGTGGTGGGGGAGAGGGAGGAAGGTAGTGAGGAGGAAGTGGGA
TGGAGGTGGTAAAGGAGGTTTCCAAGGCAGAGGAGATGGTGGTGGGAGGGGAGATTATGGTAGAAAAGATTATGGAGATC
CATATGGAGGAGGTGGTGATGGTGGTGGA

Alignment

ORF - retro_pabe_832 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.96 %
• Parental protein coverage: 52.55 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LLKIDLNSEQAEQLERINDALSCEYECRRRML-MKRLDVTVQSFGWSDRAKVKTDDIARIYQPKRYALSP
          LLKI.LN..QAEQLER.NDALSCE.EC..RML.MK.LD...QS.G..D.AKV.TDD.ARIYQPK.YALSP
Retrocopy LLKINLNLKQAEQLERVNDALSCEHECLQRML<MK*LDAAIQSVGRCDTAKVRTDDTARIYQPKCYALSP

Parental  KTTITMAHLLAAREDLSKIIRTSSGTSREKTACAINKVLMGRVPDRGGRPNEIEPPPPEMPPWQ-KRQEG
          KT.I.M.HLLAA..DLSKIIRTSSG.SR.K.ACAINKVLMGRVPDR.G.PNEIEPPP.EMPPWQ.KRQEG
Retrocopy KTAIIMVHLLAAHDDLSKIIRTSSGASR-KMACAINKVLMGRVPDREGWPNEIEPPPSEMPPWQ<KRQEG

Parental  GGGRGGWGGGGG--GGSRGGGGGGGGRGGWGGGGGWLGGGGGGGGGWGGGG-GGG-RGGFQGRGDYGGRG
          .GGRGGWGGG.G..GGSR.G.GGG.GRGGW..GGGW..GGG.GG...GG.G..GG..GGFQGRGD.GGRG
Retrocopy SGGRGGWGGGRGDRGGSRRGCGGGSGRGGW-RGGGWESGGGEGGR**GGSG<DGGGKGGFQGRGDGGGRG

Parental  GYGGRGGYGGRGYGDPYGGGGGG
          .Y.GR..YG...YG...GG.GGG
Retrocopy DY-GRKDYGD-PYGG--GGDGGG

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	18.52 RPM
SRP007412_cerebellum	0.00 RPM	19.58 RPM
SRP007412_heart	0.00 RPM	7.56 RPM
SRP007412_kidney	0.00 RPM	9.15 RPM
SRP007412_liver	0.00 RPM	4.47 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_832 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_832 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_832 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019041	1 retrocopy	retro_etel_211,
Pongo abelii	ENSPPYG00000006336	1 retrocopy	retro_pabe_832 ,
Rattus norvegicus	ENSRNOG00000005366	1 retrocopy	retro_rnor_680,