RetrogeneDB ID: retro_mdom_585

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:402435014..402436827(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000000608
• Aliases: None
• Description: None

Sequence

>retro_mdom_585
AAATACTCAATTATGAGTGTGGTAGAGGACGGTGTGCTGTTATCACATTTGATGAGTAGTGATATACATGAAATGAAATA
TGATTTGTCATGTGAACTCTACAGAATGTCTACATACTCTGTTTTCCCAGTCAATGTTCCAACCTCAGAAAGGAGTCTTG
CTCAGGTTGGATTTTATTACACTGGTATGAATGACAGAGTTAAATGTTTCTGTTGTGGCTTAATGCTGGATAACTGGAAA
CAAGGAGAGAATGCGATTGACAAACATAAACAGCTATATCCTAGCTGTGCCTTTATTCAGAATCTGGTTTCAGTTAATCT
GGGATCTTCTCAATCTACATTTTCTTCTTCAGTGAATAATGCCACATGTTCATTATCTCTCAGTTCAGAACAGAGTGGAT
ATTTCAGTGGTTCTTATTCCAGTTTTCCACTGCAGCCAGTGATTTCCAGAGGAGTTAAGGACTTGTCCCCTTTGAACACC
AGCCCCTACAGTTATTCTATGAGTACTGAAGAGGCCAGAATTCCTACTTACCAGGCATGGCCGTTGACATTTCTGTCACC
ATTAGATCTGGCAAGAGCTGGCTTTTATTATATAGGGCCTGGAGACATGGTAGCTTGCTTTGCCTGTGGCGGAAAACTAA
GTAACGGGGAACCAAAAGATGATGCCATGTCAGAGCACCAAAGACATTTTCCTCACTGTCCTTTCTTAGAGAGTCAAATC
CAAGAAAAATCAAGGTTCAATGTTCCTAATCTGAGCATGCAAACCCATGCAGCCTATGTGAAAACCTTTGTGACCTGGCC
ACCTCAAATTCCAGTTCATCCAGAGCAGCTTGCAAGTGCTGGCTTTTATTATGTGGGTCGAAATGATGATGTGAAGTGCT
TTTGCTATGATGGTGGACTGAGGTGTTGGGAATCTGGACATGATCCTTGAGTGGAACATGCCAAATGGTTCCCAAGGTGT
GAGTATTTGATACGAATGAAAGGTCAAGAGTTTGTTGACCAAGTTCAACCTAGGTACCCTCATCTCCTTGAACAGCTATT
ATCAACTTCAGATATGCCAGGAGATGAAAATGCTGATCTACCAATTATTCATTTTGGACCTGGAGAAAATAATTCAGAAG
ATACAGTCATGGTGAACACTCCAGTGATTAAAGCTGCTTTGGAAATGGGCTTCAGTAGAAGTCTAGTAAAACAGATTGTT
CAGAGTAAAATCTTAACTACTGGAGAAAATTACAAAACAGTCAATGAGGTTGTATCGGATCTCCTCAATGCAGAAGATGA
AAAAAGGAAAGAAGAGAAAGAGAGACAAACTGAAGAAATGGCATTAGATGACCTGACATTAATTCAGAAGAATAGAATGG
CTCTGTTTCAGCATTTGACCTGTGTACTTCCTATCCTGGATAGTCTCTTAACATCCAGTGTGATTAATGAGCAGGAACAT
GATGTTATTAAACAAAAAACACAGACGTCTCTACAAGCAAGAGAACTGATTGATACCATTTTAGTCAAAGGAAATGCTGC
AGCCAGTGTATTTAAAAACTGTCTCAGAGAAATTGGTTCTGTGTTATATAATAATTTATTTGTGGAAAAGAACATGAAGT
ATATTCCAGCAGAAGATGTTTCAGGTCTTCCTATGGAAGAACAACTTAAGAGATTACAAGAAGAAAGAACATGTAAAGTT
TGTATGGACAAAGGTTTCTATTATATTTATTCCTTGTGGTCATCTAGTAGTATGCAAAGAATGTGCTCCTTCTCTAAGAA
AATGCCCTATTTGCAGGGGTATAATCAAAGGTACAGTATGTGCATTTCTTTCA

Alignment

ORF - retro_mdom_585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.62 %
• Parental protein coverage: 97.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KYSIMSVVEDGVLLSHLMSSDTHEMKYDLSCELYRMSTYSAFPVNVPISERSLARAGFYYTGVNDRVKCF
          KYSIMSVVEDGVLLSHLMSSD.HEMKYDLSCELYRMSTYS.FPVNVP.SERSLA..GFYYTG.NDRVKCF
Retrocopy KYSIMSVVEDGVLLSHLMSSDIHEMKYDLSCELYRMSTYSVFPVNVPTSERSLAQVGFYYTGMNDRVKCF

Parental  CCGLMLDNWKQGDNAIDKHKQLYPSCAFIQNLISVNLGSSQSTFSSSVNNATRSLSLSSEQSGYFSGSYS
          CCGLMLDNWKQG.NAIDKHKQLYPSCAFIQNL.SVNLGSSQSTFSSSVNNAT.SLSLSSEQSGYFSGSYS
Retrocopy CCGLMLDNWKQGENAIDKHKQLYPSCAFIQNLVSVNLGSSQSTFSSSVNNATCSLSLSSEQSGYFSGSYS

Parental  SFPLEPVTSRGVEDLSPLNTSPYSYSMSTEEARILTYQAWPLTFLSPLDLARAGFYYIGPGDMVACFACG
          SFPL.PV.SRGV.DLSPLNTSPYSYSMSTEEARI.TYQAWPLTFLSPLDLARAGFYYIGPGDMVACFACG
Retrocopy SFPLQPVISRGVKDLSPLNTSPYSYSMSTEEARIPTYQAWPLTFLSPLDLARAGFYYIGPGDMVACFACG

Parental  GKLSNWEPKDDAMSEHRRHFPHCPFLESQIQETSRFNVSNLSMQTHAARVKTFVTWPPQIPVHPEQLANA
          GKLSN.EPKDDAMSEH.RHFPHCPFLESQIQE.SRFNV.NLSMQTHAA.VKTFVTWPPQIPVHPEQLA.A
Retrocopy GKLSNGEPKDDAMSEHQRHFPHCPFLESQIQEKSRFNVPNLSMQTHAAYVKTFVTWPPQIPVHPEQLASA

Parental  GFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPR-QYLIRMKGQEFVDQVQARYPHLLEQLLSTS
          GFYYVGRNDDVKCFC.DGGLRCWESG.DP.VEHAKWFPR..YLIRMKGQEFVDQVQ.RYPHLLEQLLSTS
Retrocopy GFYYVGRNDDVKCFCYDGGLRCWESGHDP*VEHAKWFPRCEYLIRMKGQEFVDQVQPRYPHLLEQLLSTS

Parental  DIPGDENAELPIIHFGPGENNSEDTVMMNTPVIKAALEMGFSRSLVKQIVQSKILTTGENYKTVNEVVSD
          D.PGDENA.LPIIHFGPGENNSEDTVM.NTPVIKAALEMGFSRSLVKQIVQSKILTTGENYKTVNEVVSD
Retrocopy DMPGDENADLPIIHFGPGENNSEDTVMVNTPVIKAALEMGFSRSLVKQIVQSKILTTGENYKTVNEVVSD

Parental  LLNAEDEKRKEEKERQTEEMASDDLTLIRKNRMALFQHLTCVLPILDSLLTSGVINEQEHDVIKQKTQTS
          LLN.................A.DDLTLI.KNRMALFQHLTCVLPILDSLLTS.VINEQEHDVIKQKTQTS
Retrocopy LLNXXXXXXXXXXXXXXXXXALDDLTLIQKNRMALFQHLTCVLPILDSLLTSSVINEQEHDVIKQKTQTS

Parental  LQARELIDTILVKGNAAASVFKNCLREIGSVLYNNLFVEKNMKYIPTEDVSGLPMEEQLRRLQEERTCKV
          LQARELIDTILVKGNAAASVFKNCLREIGSVLYNNLFVEKNMKYIP.EDVSGLPMEEQL.RLQEERTCKV
Retrocopy LQARELIDTILVKGNAAASVFKNCLREIGSVLYNNLFVEKNMKYIPAEDVSGLPMEEQLKRLQEERTCKV

Parental  CMDKEVSIVFIPCGHLVVCKECAPSLRKCP-ICRGIIKGTVRTFLS
          CMDK.................C..S..K.P.ICRGIIKGTV..FLS
Retrocopy CMDKGFYYIYSLWSSSSMQRMCSFS-KKMP>ICRGIIKGTVCAFLS

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.20 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.59 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_585 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_585 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.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035735	1 retrocopy	retro_btau_1262,
Monodelphis domestica	ENSMODG00000000608	3 retrocopies	retro_mdom_1857, retro_mdom_585 , retro_mdom_683,
Otolemur garnettii	ENSOGAG00000010377	2 retrocopies	retro_ogar_2542, retro_ogar_953,
Otolemur garnettii	ENSOGAG00000030385	1 retrocopy	retro_ogar_3331,
Ictidomys tridecemlineatus	ENSSTOG00000005734	1 retrocopy	retro_itri_426,