RetrogeneDB ID: retro_pabe_2715

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:5440477..5441183(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ppy-mir-1224
• Ensembl ID: ENSPPYG00000014350
• Aliases: None
• Description: ppy-mir-1224 [Source:miRBase;Acc:MI0015193]

Sequence

>retro_pabe_2715
AGCCTGACAGCCTCTGTGAAGATGAATGTGCTGCTCTTCGCCCCTGGGTTACTGTTTCTTCTTCTCACACAGTTTGGCTG
CCATGGGGCCTTCCGCAAGCTGGGCATTTGTGTTGGCCTTCAGGTGGTGCTGGGGCTGCCCTTCCTGCTGGAGAAGCCCA
CTGGCTACCTGTCTCGCTCCTTTGACCTTGGCCGCCAGTTTCTGTTCTGCTGGACAGTGAACCGGCGCTTCCTCCCAGGG
GCTCTCTGCCTGCACCATGCCTTCCATCTGGCCCTGCTGGCCACCCACCTCACCTTGCTCTTGCTGTTTACCCTCTACGG
GTGGCACAGGATGGGGGAATGTATCTTGTCACTGAGGAAGGATCCCTCCAAAAGGAAGGTTCCACCCCACCCCTTCATAC
CCAACCAGATCGTTTCTACCCTCTTCACCTCTAACTTCATTGGCATCTGCTTCAGCCACCCCCCTCCACTACCAGTTCTA
TGTCTGGTATTTCCACACACTGCCCTACCTCCTGTGGGCCAGGACTGCACACTGGCTCACACACCTGCTCAGGTTGCTGG
TGCTGGGGCTCATGGAGCTCTCCTGGAACACATACCCCTCCACATCCTGCAACTCTGCTGCCCAGCATGTGTGCCATGCT
ATCCTCTTACTGCAGCTCTGGCTGGGCCTGCAGCCATTCCCCAAGAGCATCCAATGCATCAAGAAA

Alignment

ORF - retro_pabe_2715 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.63 %
• Parental protein coverage: 53.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLAVSVKMNVLLFAPGLLFLLLTQFGFRGALPKLGICAGLQVVLGLPFLLENPIGYLSRSFDLGRQFLFR
          SL..SVKMNVLLFAPGLLFLLLTQFG..GA..KLGIC.GLQVVLGLPFLLE.P.GYLSRSFDLGRQFLF.
Retrocopy SLTASVKMNVLLFAPGLLFLLLTQFGCHGAFRKLGICVGLQVVLGLPFLLEKPTGYLSRSFDLGRQFLFC

Parental  WTVNWRFLPEALFLHRAFHLALLTAHLTLLLLFALCRWHRTGESILSLLRDPSKRKVPPQPLTPNQIVST
          WTVN.RFLP.AL.LH.AFHLALL..HLTLLLLF.L..WHR.GE.ILSL..DPSKRKVPP.P..PNQIVST
Retrocopy WTVNRRFLPGALCLHHAFHLALLATHLTLLLLFTLYGWHRMGECILSLRKDPSKRKVPPHPFIPNQIVST

Parental  LFTSNFIGICFSR-SLHYQFYVWYFHTLPYLLWATPARWLTHLLRLLVLGLIELSWNTYPSTSCSSAALH
          LFTSNFIGICFS...LHYQFYVWYFHTLPYLLWA..A.WLTHLLRLLVLGL.ELSWNTYPSTSC.SAA.H
Retrocopy LFTSNFIGICFSH>PLHYQFYVWYFHTLPYLLWARTAHWLTHLLRLLVLGLMELSWNTYPSTSCNSAAQH

Parental  VCHAVILLQLWLGPQPFPKSTQHSKK
          VCHA..LLQLWLG.QPFPKS.Q..KK
Retrocopy VCHAILLLQLWLGLQPFPKSIQCIKK

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	16.53 RPM
SRP007412_cerebellum	0.00 RPM	11.31 RPM
SRP007412_heart	0.00 RPM	5.06 RPM
SRP007412_kidney	0.00 RPM	17.97 RPM
SRP007412_liver	0.00 RPM	20.41 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2715 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2715 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2715 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3286
Macaca mulatta	retro_mmul_2063

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000214160	1 retrocopy	retro_hsap_3286,
Macaca mulatta	ENSMMUG00000018951	1 retrocopy	retro_mmul_2063,
Nomascus leucogenys	ENSNLEG00000006230	1 retrocopy	retro_nleu_1352,
Pongo abelii	ENSPPYG00000014350	1 retrocopy	retro_pabe_2715 ,