RetrogeneDB ID: retro_mdom_25

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:446852052..446852712(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023442
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018271
• Aliases: None
• Description: None

Sequence

>retro_mdom_25
ATGAATGGGCGGGCCCGGGTGCTGTACTTTGACAGCTGGGTGCGGGTGCTGAAGTTGGGAGAGAGTTTTGAGAAGCATCC
GCGTAGCACCTTCCACACCGTGCGTTATGACTGTAAACCTGCATCTATTGACACCTCTTGTGAAGGAGATCTTGAAGTTG
GCAAAGGTGAACAGATGACAATAACACTGCCAAATATAGAGAGTAGAAGAAGCAGTAAAATTCAGTCTCTACTAGGAAAG
CAGCAACAACAACAACAGATGAGAAATGCAGTCAAAACACCCAACAATGTGAAACACTCTCCACCAAAAGAAAAAATGTC
TCCAGAATCTCCTATGGGTGATATTGAAAGAGAACTGAAGGCAGAAGCAAGTATAATGGACCAGATGACTAGTTCTGATA
GCTCTTCAGAATCCCAAAGTTCTTCATCTTCAAGTAGTGAAGATGGTTCTAGTGACTCAGAAGATGAAGGGTGCAAAAAC
TCTCATTCTAACTCAGTAAAATGTGTACTTGTCCATCAAACCTCATCTGCTAAACCAAAACAATGGATGCCTGATACAGA
GGCCATGCAGAACAGATCTCACAATGGAAGTGGCCTTCTGATAAATACATTAAGAAACGATTTGCAGTTGAGTGAATCAG
GAAGTGACAGCGATGAATGA

Alignment

ORF - retro_mdom_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.82 %
• Parental protein coverage: 59.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITVKKTRVEGSSKIQSLLGKQQQQQ-MRNAVKTPNNVKHFPPKEKMSPESPMDDIERELKAEASIMDQMT
          IT........SSKIQSLLGKQQQQQ.MRNAVKTPNNVKH.PPKEKMSPESPM.DIERELKAEASIMDQMT
Retrocopy ITLPNIESRRSSKIQSLLGKQQQQQQMRNAVKTPNNVKHSPPKEKMSPESPMGDIERELKAEASIMDQMT

Parental  SSDSSSESQSSSSSSSEDGSSDSEDEGCKNSHSNSVKCVPVHQTSSAEPKQWMPDTEAMQNRSHNGSGLL
          SSDSSSESQSSSSSSSEDGSSDSEDEGCKNSHSNSVKCV.VHQTSSA.PKQWMPDTEAMQNRSHNGSGLL
Retrocopy SSDSSSESQSSSSSSSEDGSSDSEDEGCKNSHSNSVKCVLVHQTSSAKPKQWMPDTEAMQNRSHNGSGLL

Parental  INTLRNDLQLSESGSDSDE
          INTLRNDLQLSESGSDSDE
Retrocopy INTLRNDLQLSESGSDSDE

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	0.12 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	0.50 RPM	0.00 RPM
SRP007412_testis	0.39 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_25 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_25 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006427	1 retrocopy	retro_cpor_235,
Felis catus	ENSFCAG00000018226	1 retrocopy	retro_fcat_1398,
Macropus eugenii	ENSMEUG00000005416	1 retrocopy	retro_meug_1621,
Monodelphis domestica	ENSMODG00000014543	1 retrocopy	retro_mdom_290,
Monodelphis domestica	ENSMODG00000018271	1 retrocopy	retro_mdom_25 ,
Tupaia belangeri	ENSTBEG00000017542	1 retrocopy	retro_tbel_4110,