RetrogeneDB ID: retro_mdom_466

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:702896792..702897650(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IL1R1
• Ensembl ID: ENSMODG00000002332
• Aliases: None
• Description: interleukin 1 receptor, type I [Source:HGNC Symbol;Acc:5993]

Sequence

>retro_mdom_466
ATAATGAATTTGTTTTGGTATGCTAGCTTCATAATTCTACTGATTTCTCCTCTTGAAGCTGATAATTGTGTGGAGGTTGA
AGCACAACTAATCTTAGTTATTTTTGAAGATGAACTTGATGTTCATCAGTTTGGTCAAAGAGCATTTGACTCTTAACGTA
ATCGAAGTTGGTATGGAAGTGATGGTAAGACACTCATCTCAATGGATCAGAACTCTAGGGCTCACCAATACAGAGAGATA
CTTTGGTTTGCTCCAGCTGCAACAGAGGATACAGGATATTATTACTGTGTTGAAAGAAATTCTACCCACTGCCACAAAGA
GAAATTCAAGATAGAAATTTTGAAGAAAAATCCTGGAATATGTCATAATGAGCAAAATGATTATATTAAAAAATTGCCTA
TAGGACCCGGTGGCTTCATTGTGTGTACCCATTTGGATATTTTTAAAGATGAAAATAATAATCTACCTAAAGTACAGTGG
TATAAGGATTGGAAACCTCTTCTTGACACAAGATTTCAAGGAAAAAAGAAAGATCTTTTCCTGGATGACATACAGAAAGT
GGATCAGGGGCACTATACCTGCCTTATATCCTATCCTTATATAGGGAAGCATTATAATGTTACTCGGTCAATTCATCTAA
GTATTATGGGATCAGGAAAGAAAAAACTACCAACAATTCTGGCACCTGAAAACAAGACAATGGAGGTAGAACTTGGGTCC
TGGTTGCTTTTGGACTGCAATTTCACAGTTGGAAAGAACCAATATCCCTATTGGTCTTGGAATGGATCATATGCTGACAT
TGATCCCAATATTGCATGGTTTACGCCTCAAATCCCAAATTTAACCAAAACGAATCCC

Alignment

ORF - retro_mdom_466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.15 %
• Parental protein coverage: 50.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMNLFWYASFIILLISPLEADNCVEVEAQLILVIFEDELDVRQCGQRAFDSYSNRTWYGSDGKTLISMDQ
          .MNLFWYASFIILLISPLEADNCVEVEAQLILVIFEDELDV.Q.GQRAFDS..NR.WYGSDGKTLISMDQ
Retrocopy IMNLFWYASFIILLISPLEADNCVEVEAQLILVIFEDELDVHQFGQRAFDS*RNRSWYGSDGKTLISMDQ

Parental  NSRVHQYREILWFAPAATEDTGYYYCVERNSTHCHKEKFKIEILKKNPGICHNEQNDYIQKLPIGPGGFI
          NSR.HQYREILWFAPAATEDTGYYYCVERNSTHCHKEKFKIEILKKNPGICHNEQNDYI.KLPIGPGGFI
Retrocopy NSRAHQYREILWFAPAATEDTGYYYCVERNSTHCHKEKFKIEILKKNPGICHNEQNDYIKKLPIGPGGFI

Parental  VCPHLDIFKDENNNLPKVQWYKDCKPLLDTRFQGKKKDLFLDDIQKVDQGHYTCLISYPYIGKHYNVTRS
          VC.HLDIFKDENNNLPKVQWYKD.KPLLDTRFQGKKKDLFLDDIQKVDQGHYTCLISYPYIGKHYNVTRS
Retrocopy VCTHLDIFKDENNNLPKVQWYKDWKPLLDTRFQGKKKDLFLDDIQKVDQGHYTCLISYPYIGKHYNVTRS

Parental  IHLSIMGSGKKKLPTILAPENKTMEVELGSRLLLDCNFTVGKNQYPYWSWNGSYADIDPNIAWFTPQIPN
          IHLSIMGSGKKKLPTILAPENKTMEVELGS.LLLDCNFTVGKNQYPYWSWNGSYADIDPNIAWFTPQIPN
Retrocopy IHLSIMGSGKKKLPTILAPENKTMEVELGSWLLLDCNFTVGKNQYPYWSWNGSYADIDPNIAWFTPQIPN

Parental  LTKTNP
          LTKTNP
Retrocopy LTKTNP

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_466 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_466 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	ENSMODG00000002332	1 retrocopy	retro_mdom_466 ,