RetrogeneDB ID: retro_mdom_1308

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:367237853..367238876(+)
• Located in intron of: ENSMODG00000010782

Retrocopy information

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

Parental gene information

• Parental gene symbol: OXA1L
• Ensembl ID: ENSMODG00000005347
• Aliases: None
• Description: oxidase (cytochrome c) assembly 1-like [Source:HGNC Symbol;Acc:8526]

Sequence

>retro_mdom_1308
GTAGTTCCAGGTGGAGCTGCTGATGCAGTCCAGACTGCCACAGAGCAGAGCCTAAGTGACCTTGGACTAGGAGGCTTCAC
CCCAGTGGGACTCGTGGAGAACCTTTTGGAGTTTGTACATGTTGATCTGGGCCTGCCATGGTGGGGAGCCATTGTAACAT
ACACTGTTGTTGCAAGAATCATGATTTCCCCCCTCCTTGTGAAAGGCCAATGGGAGGCAGTGAAGATCAATAACCACATG
CCTGAGATTCACAAATTTTCCACCCGAATGAATGAGGCCAAGTTATCAGGGGACAAATTTGAATTTTCCAGGGCCTTTTC
AGAACTACAGCTTTACCAGAAGAAACATAATGTGAGTCCTATGAGAGGATTCATTGTTCCCCTAGACCAGGCTCCTATAT
TCATTTCCTTCTTCATTGCACTGAGAGAAATGGCCTATTTCCCTGTGCCCAGCATGCAGAATGGTGGTCTCTGATGGTTC
CAGGATCTCACAGCAGCTGATCCCCTATATGCATTGCCCGTTAGTCACAGCATCAATGTGGGCAATCCTGGAGCTGGGTG
CTGAAACTGGTGTCAACAATGCCAACCTTTGTATGATGAAAACTGTCTTCCAAGTGCTGCCCCTGATATTCTTGCCTTTT
ACCATCAATTTCCCCATTGCAGTGTTCACATACTGGTTCTCTTCCAACCTCTTCTCGTTGGCCCAAGTGAGTTTCCTGCA
GATCCCAGCTGTACGTATTTGGCTTCAAATTCCAAAGCGAATCATACATGAGCCAAGTCAGTTGCCTACACAGAAGGACC
TCATTAAGAGCATCAAAACAGGCTGGAAAAATGCCCAGACAGATCACCAGCTAAAGGAGCAGGAATGCTGCATGAGGGAT
AACCTGCAGCTTGCAGCTCGAGGTCCCTTACACAGACCTTTACCCACAACACCTTGTTATAGCCTGAAGGTAAACAGCCT
CCTACTACCACCAGTACCAGCAGTAAACCAAAGTCACAGAAGCCCTGGAGGGATACTCTTGGA

Alignment

ORF - retro_mdom_1308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.53 %
• Parental protein coverage: 77.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVPGGAADAVQAATEQSLSDLGLGGFTPVGLVQNLLEFVHVDLGLPWWGAIVTCTVVARIMIFPLIVKGQ
          VVPGGAADAVQ.ATEQSLSDLGLGGFTPVGLV.NLLEFVHVDLGLPWWGAIVT.TVVARIMI.PL.VKGQ
Retrocopy VVPGGAADAVQTATEQSLSDLGLGGFTPVGLVENLLEFVHVDLGLPWWGAIVTYTVVARIMISPLLVKGQ

Parental  REAVKINNHMPEIQKFSTRMNEAKLSGDKFEFSRAFSELQLYQKKHDVSPLRGFIVPLAQAPVFISFFIA
          .EAVKINNHMPEI.KFSTRMNEAKLSGDKFEFSRAFSELQLYQKKH.VSP.RGFIVPL.QAP.FISFFIA
Retrocopy WEAVKINNHMPEIHKFSTRMNEAKLSGDKFEFSRAFSELQLYQKKHNVSPMRGFIVPLDQAPIFISFFIA

Parental  LREMAYLPVPSMQNGGLWWFQDLTAAD-PLYALPLLVTASMWAILELGAETGVNNANLRMMKTVFRVLPL
          LREMAY.PVPSMQNGGL.WFQDLTAAD.P....PL.VTASMWAILELGAETGVNNANL.MMKTVF.VLPL
Retrocopy LREMAYFPVPSMQNGGL*WFQDLTAAD>PYMHCPL-VTASMWAILELGAETGVNNANLCMMKTVFQVLPL

Parental  IVLPFTINFPTAVFTYWFSSNLFSLAQVSFLQIPAVRIWLRIPKRITHEPSQLPTQEGLIKSIKTGWKNA
          I.LPFTINFP.AVFTYWFSSNLFSLAQVSFLQIPAVRIWL.IPKRI.HEPSQLPTQ..LIKSIKTGWKNA
Retrocopy IFLPFTINFPIAVFTYWFSSNLFSLAQVSFLQIPAVRIWLQIPKRIIHEPSQLPTQKDLIKSIKTGWKNA

Parental  QTAHQLKERERRMRDHLQLAARGPLR-QTFTHNPLLQPEGKQPPTTTSTSSKPKSQKPWRDTLG
          QT.HQLKE.E..MRD.LQLAARGPL..QTFTHN.LL.PEGKQPPTTTSTSSKPKSQKPWRDTLG
Retrocopy QTDHQLKEQECCMRDNLQLAARGPLH<QTFTHNTLL*PEGKQPPTTTSTSSKPKSQKPWRDTLG

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	16.69 RPM
SRP007412_cerebellum	0.00 RPM	42.44 RPM
SRP007412_heart	0.00 RPM	71.97 RPM
SRP007412_kidney	0.00 RPM	71.11 RPM
SRP007412_liver	0.00 RPM	61.43 RPM
SRP007412_testis	0.00 RPM	23.77 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1308 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1308 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000012893	1 retrocopy	retro_mluc_2461,
Monodelphis domestica	ENSMODG00000005347	1 retrocopy	retro_mdom_1308 ,
Oryctolagus cuniculus	ENSOCUG00000000720	1 retrocopy	retro_ocun_367,
Otolemur garnettii	ENSOGAG00000000631	1 retrocopy	retro_ogar_2369,
Ictidomys tridecemlineatus	ENSSTOG00000003318	1 retrocopy	retro_itri_352,