RetrogeneDB ID: retro_pabe_2332

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:112006927..112007687(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FECH
• Ensembl ID: ENSPPYG00000009182
• Aliases: None
• Description: ferrochelatase, mitochondrial [Source:RefSeq peptide;Acc:NP_001126366]

Sequence

>retro_pabe_2332
AAGATTCAAGGGCAGTACCACAGAACTGGAGGTGGGTCCTCCATCAAGACGTGGATTTCCAAGCAGGGAGAAGGCATGGT
GAAGCTGCTGGATGACTTGTCCCTCTACACAGCCCCTCACAAATACTTCATTGGATTTTGGTATGTCCATTCTTTACCAA
AAGAAGCAAATGAAAAGATGGAGAGAAATGGCCTGGAAAGGGCTATTGCTTTCATGCAGCATCCACAGTACAGTTGCTGT
ACCACAGGCGGCAGCTTAAATGCCATTTAAAGATCCTATAACAGAGTGGGACAGAAGCTTACAATGAAGTGCAGCACTAT
CAATAGGTGGCCCACACATCGCCCCCTCACCCACTGCTTTGTTGACCACGTTCTGAAAGAGCTGGACCATTTTCCACTGG
AGAAGAGAAGCGAGTTGGCCATTCTCTTTTCTGCTCACTCACTGCCAATATCCATGATCAACAGAGGAGACCCCTATTCT
CAGGAGTTAAGTGCCACTATCCAAAGAGTCATAGAAAGGCTGCGTTACTGCAACCCTTACCAGCTGGTGTGAGGATCCAA
GGTTGGTTCAATGCCCTGGTTGGGTCTTCAAACAGATGAAATCTATCAGAGGGCTTTCTGAGAGGGGGAAGAAGAATATC
CTCTCAGTTTTGATAGCATTTACCAGTGATAACACTGAAATGCTGTGGAAACTGGATATCGAGTACTCTCAAGTTTTAGA
CAATGAGTGTGGAGTTGAAAACATCAGAAGAGCAGCCTCT

Alignment

ORF - retro_pabe_2332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.41 %
• Parental protein coverage: 59.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KIQEQYRRIGGGSPIKIWTSKQGEGMVKLLDELSPNTAPHKYYIGFRYVHPLTEEAIEEMERDGLERAIA
          KIQ.QY.R.GGGS.IK.W.SKQGEGMVKLLD.LS..TAPHKY.IGF.YVH.L..EA.E.MER.GLERAIA
Retrocopy KIQGQYHRTGGGSSIKTWISKQGEGMVKLLDDLSLYTAPHKYFIGFWYVHSLPKEANEKMERNGLERAIA

Parental  FTQYPQYSCSTTGSSLNAIYRYYNQVERKPTMKWSTIDRWPTHHLLIQCFADHILKELDHFPLEKRSEVV
          F.Q.PQYSC.TTG.SLNAI.R.YN.V..K.TMK.STI.RWPTH..L..CF.DH.LKELDHFPLEKRSE..
Retrocopy FMQHPQYSCCTTGGSLNAI*RSYNRVGQKLTMKCSTINRWPTHRPLTHCFVDHVLKELDHFPLEKRSELA

Parental  ILFSAHSLPMSVVNRGDPYPQEVSATVQNVMERLEYCNPYRLVWQSKVGPMPWLGPQTDE-SIKGLCERG
          ILFSAHSLP.S..NRGDPY.QE.SAT.Q.V.ERL.YCNPY.LV..SKVG.MPWLG.QTDE.SI.GL.ERG
Retrocopy ILFSAHSLPISMINRGDPYSQELSATIQRVIERLRYCNPYQLV*GSKVGSMPWLGLQTDE>SIRGLSERG

Parental  RKNILLVPIAFTSDHIETLYELDIEYSQVLAKECGVENIRRAES
          .KNIL.V.IAFTSD..E.L..LDIEYSQVL..ECGVENIRRA.S
Retrocopy KKNILSVLIAFTSDNTEMLWKLDIEYSQVLDNECGVENIRRAAS

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	21.95 RPM
SRP007412_cerebellum	0.00 RPM	15.56 RPM
SRP007412_heart	0.00 RPM	19.66 RPM
SRP007412_kidney	0.00 RPM	28.44 RPM
SRP007412_liver	0.00 RPM	20.20 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2332 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2332 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2332 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2631
Pan troglodytes	retro_ptro_1776
Gorilla gorilla	retro_ggor_1841
Macaca mulatta	retro_mmul_1485

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003873	1 retrocopy	retro_cjac_4008,
Homo sapiens	ENSG00000066926	1 retrocopy	retro_hsap_2631,
Gorilla gorilla	ENSGGOG00000005554	1 retrocopy	retro_ggor_1841,
Macaca mulatta	ENSMMUG00000022568	1 retrocopy	retro_mmul_1485,
Nomascus leucogenys	ENSNLEG00000008062	1 retrocopy	retro_nleu_643,
Oryctolagus cuniculus	ENSOCUG00000003020	1 retrocopy	retro_ocun_497,
Pongo abelii	ENSPPYG00000009182	1 retrocopy	retro_pabe_2332 ,
Pan troglodytes	ENSPTRG00000010045	1 retrocopy	retro_ptro_1776,