RetrogeneDB ID: retro_pabe_959

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:110084467..110085177(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOBEC3B
• Ensembl ID: ENSPPYG00000011831
• Aliases: None
• Description: apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B [Source:HGNC Symbol;Acc:17352]

Sequence

>retro_pabe_959
GCCAGCATGAAGATCGTGAACTATGATGAATTTCAACACTGTTGGGACAAATTTGTGTACAACCAAAGAATGCTATTTGA
TCCTTGGAAGCAACTGAATACAAATTACGCATTACTGCCCAGCATGCTGGGGGAGATTCTCAGACACCTGGTGGATCCAA
GAACATTCACTTACAACTTTACCAATGACCCTTCAGTCTCTGGGCAGCACCATACCTACCTGTGCTACAAGGTGGAGTGC
CAAAACAATGACACCTGGGTCTCTCTGGACCAGCACAAGGGCATCCTACCCAACCAGGCTTTGAATAATCTCAGTTGCTA
TTAAGATTTCCAAGCAGAGCAGTGCTTCCTGTACCTAACTTCCTTTGGGAGGCTGGACCGGGCTCAGTGCTACAGGGTCA
CCTGGTTCATCTCCTGGAGTCCCTGCTTCAGCTGTTCCCAGCAAGTGGCTACATTTCATTGGGAGAACAGACGTGTGAGC
CTGCACATCTTCGCTGCCCACATCTATAATTATCTCCCAGGATATGAGGGGCTGTGCACACTGCAGAGGGCTGGGACCCA
AATCTCCATCATGACCTCCAAAAGTTTAGGCACTGCTGGGTCTCCTTTGTGGACCACAAGGGATGTCCCTTCCAGCCCTG
GAATGGACTAGATGATCACAGTCAAGCCCTAAGTGGGAGGCTGCAGGCCATTCTCCAGAATCAGGAAAAC

Alignment

ORF - retro_pabe_959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.68 %
• Parental protein coverage: 62.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AHVKIMDYEEFAYCWENFVYNEGQPFMPWYKFDDNYAFLHHTLKEILRQLMDPDTFTFNFNNDPFVLRRH
          A..KI..Y.EF..CW..FVYN....F.PW.....NYA.L...L.EILR.L.DP.TFT.NF.NDP.V...H
Retrocopy ASMKIVNYDEFQHCWDKFVYNQRMLFDPWKQLNTNYALLPSMLGEILRHLVDPRTFTYNFTNDPSVSGQH

Parental  QTYLCYEVEHLDNGTWVKMDQHRGSLHNQARNPLYGLDGRHAELRFLGLLPYWQLDPAQIYRVTWFISWS
          .TYLCY.VE...N.TWV..DQH.G.L.NQA.N.L.......AE..FL.L.....LD.AQ.YRVTWFISWS
Retrocopy HTYLCYKVECQNNDTWVSLDQHKGILPNQALNNLSCY*DFQAEQCFLYLTSFGRLDRAQCYRVTWFISWS

Parental  PCFSWGCARQVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMT-YDEFEYCWNTFVDH
          PCFS..C..QV..F..EN..V.L.IFAA.IY.Y.P.Y.E.L..L..AG.Q.SIMT....F..CW..FVDH
Retrocopy PCFS--CSQQVATFHWENRRVSLHIFAAHIYNYLPGY-EGLCTLQRAGTQISIMT<LQKFRHCWVSFVDH

Parental  QGCPFQPWDGLEEHSQALSGKLQAILLNQGN
          .GCPFQPW.GL..HSQALSG.LQAIL.NQ.N
Retrocopy KGCPFQPWNGLDDHSQALSGRLQAILQNQEN

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.06 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.20 RPM
SRP007412_liver	0.03 RPM	0.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_959 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_959 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_959 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_900

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000006721	1 retrocopy	retro_ggor_900,
Pongo abelii	ENSPPYG00000011831	1 retrocopy	retro_pabe_959 ,