RetrogeneDB ID: retro_mmul_1485

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:177312316..177313290(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FECH
• Ensembl ID: ENSMMUG00000022568
• Aliases: None
• Description: Ferrochelatase [Source:UniProtKB/TrEMBL;Acc:F6ZKY9]

Sequence

>retro_mmul_1485
TCAGGTGTCACAGAAACAGCCCAGCGTGGCCAGGGTGCAAAACCTCAAGTTCAAGTGGAGAAGAGGAAGCTGAAAACTGA
AATATTAATGCTAAACATGGGAGGACCTGAAACCCTCGGACATGTTCATGACTTCCTTCTGAGGCTCTTCTTGGACCAAG
ACCTCATGACACTTACTGTTCAAAATAAGTTTACACCATTCTTTTCCAAACGCAGAACCTCCAAGATTCAAGGGCAGTAC
CACAGAATTGGAGGTGGGTTTCCCATCAAGATGTGGATTTCCAAGCAAGGAAAAGGTATGGTGAAGCTGCTGGATGACTT
GTCCCCCCACACAGCCCCTCACAAATACTTTATTGGATTTTGGCATTTCCATTCTTTACCAAAATAAGCAAATGAAGAGA
TGGAGAGAGATGACCTGGAAAGGGCTATTGCTTTCATGCAACATCCACAGTACAGTTGCTGTACCACAGGCAGCAGCTTA
AATGCCATTTAAAGATCAGATAATAGAGTGGGACAGAAGCTTACAATGAAGTGGAGCACTATCGGCAGGTGGCCCACACA
TCGCCTCCTCACCCATTGCTTTGCTGACCACATTCTGAAAGAGCTGGATCATTTTCCACTGGAGAAGAGAAGTGAGTTGG
CCATTCTCTTTTCTGTTCACTTTTCTGCCAATATCCGTGTTCAACAGAGGAGACCCCTATTCTTAGGAGTTGTGTACCAC
TATCCAAAGAGTCATAGAAAGGCTGGGTTACTGCAACCCTTACCAGCTGGTGTGAGAATCCAAGGTTGGTTCAATGCCCT
GGTTGGATCTTCAAAGAGATAAAATCTATCAGAGGGCTTTCTGAGAGGGGAAAGAAGAATATCCTCTCAGTTTTCATAGC
ATTTACCAATGATAACACCAAAATGCTGTAGAAACTGGATATCGAGTACTCTCAAGTTTTAGACCATGAGTGTGGAGTTG
AAAACATCAGAAAA

Alignment

ORF - retro_mmul_1485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.78 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAATETAQHAQHAKPQVQPQKRYESNIRKPKTGILMLNMGGPETLGDVHDFLLRLFLDRDLMTLPIQNKL
          ...TETAQ..Q.AK....PQ...E...RK.KT.ILMLNMGGPETLG.VHDFLLRLFLD.DLMTL..QNK.
Retrocopy SGVTETAQRGQGAK----PQVQVEK--RKLKTEILMLNMGGPETLGHVHDFLLRLFLDQDLMTLTVQNKF

Parental  APFIAKRRTPKIQEQYRRIGGGSPIKIWTSKQGEGMVKLLDELSPNTAPHKYYIGFRYVHPLTEEAIEEM
          .PF..KRRT.KIQ.QY.RIGGG.PIK.W.SKQG.GMVKLLD.LSP.TAPHKY.IGF...H.L...A.EEM
Retrocopy TPFFSKRRTSKIQGQYHRIGGGFPIKMWISKQGKGMVKLLDDLSPHTAPHKYFIGFWHFHSLPK*ANEEM

Parental  ERDGLERAIAFTQYPQYSCSTTGSSLNAIYRYYNQVGRKPTMKWSTIDRWPTHHLLIQCFADHILKELDH
          ERD.LERAIAF.Q.PQYSC.TTGSSLNAI.R..N.VG.K.TMKWSTI.RWPTH.LL..CFADHILKELDH
Retrocopy ERDDLERAIAFMQHPQYSCCTTGSSLNAI*RSDNRVGQKLTMKWSTIGRWPTHRLLTHCFADHILKELDH

Parental  FPLEKRSEVVILFSAH-SLPMSVVNRGDPYPQEVSATVQNVMERLGYCNPYRLVWQSKVGPMPWLGPQTD
          FPLEKRSE..ILFS.H..LP.SV.NRGDPY..E...T.Q.V.ERLGYCNPY.LV..SKVG.MPWL..Q.D
Retrocopy FPLEKRSELAILFSVH>FLPISVFNRGDPYS*ELCTTIQRVIERLGYCNPYQLV*ESKVGSMPWLDLQRD

Parental  -ESIKGLCERGRKNILLVPIAFTSDHIETLYELDIEYSQVLAKECGVENIRR
          ..SI.GL.ERG.KNIL.V.IAFT.D....L..LDIEYSQVL..ECGVENIR.
Retrocopy >KSIRGLSERGKKNILSVFIAFTNDNTKML*KLDIEYSQVLDHECGVENIRK

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	0.00 RPM	13.33 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	16.10 RPM
SRP007412_cerebellum	0.00 RPM	14.27 RPM
SRP007412_heart	0.00 RPM	17.02 RPM
SRP007412_kidney	0.00 RPM	26.17 RPM
SRP007412_liver	0.00 RPM	27.27 RPM
SRP007412_testis	0.00 RPM	7.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1485 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1485 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
Pongo abelii	retro_pabe_2332

---

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,