RetrogeneDB ID: retro_mdom_265

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:33345668..33346142(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000011762
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025514
• Aliases: None
• Description: None

Sequence

>retro_mdom_265
CTTGGCCCCGATGCTGCTGCAGGCCCGGAGCGCCGGGGCGGCCGCCTAGAGCAGCAGCGGCTCCAGGAGCAGAAGCCGCG
GTGGCGGGACGCGCAACAGAGGCACCAGCTGCAGCACCTCGAGTCCTTTTATGAAAAGCCTCCTCCTGGACTTATTAAGG
AAGATGAGACTAAGCCAGAAGACTGTATCCCAGATGTACCAGGCAATGAACACGCCAGAGAATTTCTGGCTCATGCTCCA
ACTAAAGGGCTCTGGATGCCCCTGGGGAAAGAAGTCAAGGTTATGCAATGCTGGCGCTGTAAACGGTATGGACACAGAAC
AGGTGACAAAGAATGCCCATTCTTTATCAAAGGCAATCAGAAATTAGAACAATTCAGAGTAGCACACGAAGATCCCATAT
ATGACATCATAAGAGAGAATAAGCGGCATGAAAAGGATGTGAGGATACAGCAGTTAAAGAAGCTACTAGAAGAT

Alignment

ORF - retro_mdom_265 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.92 %
• Parental protein coverage: 70.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REAAELEQQRRQEQKRRRRDAQQRQQLQHLESFYEKPPPGLIKEDETKPEDCIPDVPGNEHAREFLAHAP
          R....LEQQR.QEQK.R.RDAQQR.QLQHLESFYEKPPPGLIKEDETKPEDCIPDVPGNEHAREFLAHAP
Retrocopy RRGGRLEQQRLQEQKPRWRDAQQRHQLQHLESFYEKPPPGLIKEDETKPEDCIPDVPGNEHAREFLAHAP

Parental  TKGLWMPLGKEVKVMQCWRCKRYGHRTGDKECPFFIKGNQKLEQFRVAHEDPMYDIIRENKRHEKDVRIQ
          TKGLWMPLGKEVKVMQCWRCKRYGHRTGDKECPFFIKGNQKLEQFRVAHEDP.YDIIRENKRHEKDVRIQ
Retrocopy TKGLWMPLGKEVKVMQCWRCKRYGHRTGDKECPFFIKGNQKLEQFRVAHEDPIYDIIRENKRHEKDVRIQ

Parental  QLKKLLED
          QLKKLLED
Retrocopy QLKKLLED

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_265 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_265 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 4 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025514	17 retrocopies	retro_mdom_1205, retro_mdom_1515, retro_mdom_1553, retro_mdom_1622, retro_mdom_1759, retro_mdom_1840, retro_mdom_1905, retro_mdom_1912, retro_mdom_265 , retro_mdom_317, retro_mdom_386, retro_mdom_560, retro_mdom_623, retro_mdom_687, retro_mdom_761, retro_mdom_818, retro_mdom_896,
Oryctolagus cuniculus	ENSOCUG00000029333	1 retrocopy	retro_ocun_1635,
Sarcophilus harrisii	ENSSHAG00000001730	2 retrocopies	retro_shar_440, retro_shar_650,
Tupaia belangeri	ENSTBEG00000009535	1 retrocopy	retro_tbel_280,