RetrogeneDB ID: retro_mdom_1174

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:357071850..357072699(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YARS
• Ensembl ID: ENSMODG00000017404
• Aliases: None
• Description: tyrosyl-tRNA synthetase [Source:HGNC Symbol;Acc:12840]

Sequence

>retro_mdom_1174
GCCTTCTGTGAGCCAGGGAATGTGGAAAACAATGGAGTCTTAGCCTTCATCAGACATGTGCTTTTCCCTCTGAAGTCAGA
GTTTGTGATTCTTCAAGATGAGAAGTGGGGTGGCAATAAAGCCTACATGGCTTACTCATAGCTGGAAAAGGACTTTGCCA
ACCAGGTGGTCCATCCTGGAGACCTGAAGAATGCAGTTGAAGTTGCCTTGAACAAATTACTGGACCCCATTCGGGAAAGA
TTTAATGTACCTGCTTTGAAGAAGCTATCCAGTGCAGCTTACCCTGACTTAACAAAACAGAAGTCGATGGCCAAAGGCTG
TGCCAAGAACTAGGAGCCAGAAGAGGTCATCCCATCCCAACTGGATATCCGTGTAGGGAAAGTGATCAGTGTGGAGAAGC
ACCCCAATGCAGATAGTCTGTACCTGGAGAAGATTGATGTTGGGGAGCCTGAGCAATGGACAGTGGTGAGTGGCCTGGTT
CAGTTTGTTCTCAAGGAGGAACTACAGGACAGACTTGTGGTGGTCCTGTGCAACTTGAAACCCCCCAAAATAAGAGGAGT
AGAGTCACAAGGGATGCTTCTCTGTGTGTCCATGGAAGGGGCAAACCTCCAGGTGGAGCTCCTAGACCCTCCTTCAGGCT
CAGCCCCTGGGGAGCATGTGTTTGTGTTTGTGGAGGGATATGAGAAGGGCCAATCTGATGAAGAGCTCAAACCCAAGAAA
AAAGTATTTGAGAAACTCCAGGCTGACTTTAAAATCTCATCAGAGTGCATTGCACAATGGAAGCAAACCAACATCATGAC
CAAGCTGGGCTTCATCTCTTGTAAAACACTTAAGGGAGGAAGCATTAGC

Alignment

ORF - retro_mdom_1174 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.81 %
• Parental protein coverage: 53.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFCEPGNVENNGVLAFIRHVLFPLKSEFVILRDEKWGGNKTYTAYSELEKDFANQVVHPGDLKNSVEVAL
          AFCEPGNVENNGVLAFIRHVLFPLKSEFVIL.DEKWGGNK.Y.AYS.LEKDFANQVVHPGDLKN.VEVAL
Retrocopy AFCEPGNVENNGVLAFIRHVLFPLKSEFVILQDEKWGGNKAYMAYS*LEKDFANQVVHPGDLKNAVEVAL

Parental  NKLLDPIRERFNAPALKKLSSAAYPDLTKQKPMAKGCAKNSEPEEVIPSRLDIRVGKVISVEKHPDADSL
          NKLLDPIRERFN.PALKKLSSAAYPDLTKQK.MAKGCAKN.EPEEVIPS.LDIRVGKVISVEKHP.ADSL
Retrocopy NKLLDPIRERFNVPALKKLSSAAYPDLTKQKSMAKGCAKN*EPEEVIPSQLDIRVGKVISVEKHPNADSL

Parental  YLEKIDVGEPEPRTVVSGLVQFVPKEELQDRLVVVLCNLKPQKMRGVESQGMLLCASMEGTNRQVELLDP
          YLEKIDVGEPE..TVVSGLVQFV.KEELQDRLVVVLCNLKP.K.RGVESQGMLLC.SMEG.N.QVELLDP
Retrocopy YLEKIDVGEPEQWTVVSGLVQFVLKEELQDRLVVVLCNLKPPKIRGVESQGMLLCVSMEGANLQVELLDP

Parental  PSGSAPGER--VFVEGYDKGQPDDELKPKKKVFEKLQADFKISSECIAQWKQTNFMTKLGFVSCKTLKGG
          PSGSAPGE...VFVEGY.KGQ.D.ELKPKKKVFEKLQADFKISSECIAQWKQTN.MTKLGF.SCKTLKGG
Retrocopy PSGSAPGEHVFVFVEGYEKGQSDEELKPKKKVFEKLQADFKISSECIAQWKQTNIMTKLGFISCKTLKGG

Parental  SIS
          SIS
Retrocopy SIS

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	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1174 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1174 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000017404	1 retrocopy	retro_mdom_1174 ,