RetrogeneDB ID: retro_mdom_290

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:60335128..60335911(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025072
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000014543
• Aliases: None
• Description: None

Sequence

>retro_mdom_290
ATGAACGGCACCGCGAACCCGCTGCTGGACCGCGAGGAGCACGGCCTGAAGCTCGGCGAGAGCTTCGAGAAGAGGCCGAA
GTCGTCCTTCCACACCATCCGCTATGATTTTAAGCCAGCATCTATAGATACTTCATGTGAAGGAGAACTCCAAGTTGGCA
AGGGAGATGAAGTCACAATTACACTTCCACATATTCCTGGATCAACACCTCCAATGACTGTGTTCAAAGGAAACAAAAGG
CCCTATCAGAAAGACTGTGTTCTCATCATTAATCATGATACTGGGGAATATGTATTGGAAAAGCTCAGTAGCAGCATTCA
GGTCAAGAAAACAAGAGCTGAAGGAAGCAGCAAAATCCAGGCCCGAATGGAGCAGCCCCCTTCTCGAGCACCACCACCTC
CTGTGCCATTCAGAGCCCCAATGAAACCACCAATTGGACCAAAAACATCCCCTGTGAAAGATAATCCTTCACCTGAACCT
CAATTGGATGACATTAAAAGAGAGCTAAGAGCAGAGGTTGAAATCATTGAGCAGATGAGCAGCAGCAGCGGGAGCAGCTC
CTCAGATTCTGAGAGCTCTTCAGGCAGTGACGATGATAGCTCCAGCAGTGGAGGAGAAGAGCCAGCTGCCCGCGCCTCAC
CCTCCCAGCCTCCTCACCAGCAGTTCAGTCACAGGAACCCCATGGCCAATGGCACCAGCCGGCCCTCTGGAAATCACCAG
CTGATGAACACCCTTCGAAATGACTTACAATTGAGTGAATCTGGCAGTGACAGTGATGACTAG

Alignment

ORF - retro_mdom_290 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGTANPLLDREEHGLKLGESFEKRPKSSFHTIRYDFKPASIDTSCEGELQVGKGDEVTITLPHIPGSTP
          MNGTANPLLDREEHGLKLGESFEKRPKSSFHTIRYDFKPASIDTSCEGELQVGKGDEVTITLPHIPGSTP
Retrocopy MNGTANPLLDREEHGLKLGESFEKRPKSSFHTIRYDFKPASIDTSCEGELQVGKGDEVTITLPHIPGSTP

Parental  PMTVFKGNKRPYQKDCVLIINHDTGEYVLEKLSSSIQVKKTRSEGSSKIQARMEQPPSRAPPPPVPFRAP
          PMTVFKGNKRPYQKDCVLIINHDTGEYVLEKLSSSIQVKKTR.EGSSKIQARMEQPPSRAPPPPVPFRAP
Retrocopy PMTVFKGNKRPYQKDCVLIINHDTGEYVLEKLSSSIQVKKTRAEGSSKIQARMEQPPSRAPPPPVPFRAP

Parental  MKPPIGPKTSPVKDNPSPEPQLDDIKRELRAEVEIIEQMSSSSGSSSSDSESSSGSDDDSSSSGGEEPAA
          MKPPIGPKTSPVKDNPSPEPQLDDIKRELRAEVEIIEQMSSSSGSSSSDSESSSGSDDDSSSSGGEEPAA
Retrocopy MKPPIGPKTSPVKDNPSPEPQLDDIKRELRAEVEIIEQMSSSSGSSSSDSESSSGSDDDSSSSGGEEPAA

Parental  RASPSQPPHQQFSHRNPMANGTSRPSGNHQLMNTLRNDLQLSESGSDSDD
          RASPSQPPHQQFSHRNPMANGTSRPSGNHQLMNTLRNDLQLSESGSDSDD
Retrocopy RASPSQPPHQQFSHRNPMANGTSRPSGNHQLMNTLRNDLQLSESGSDSDD

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	4.77 RPM	0.00 RPM
SRP007412_cerebellum	5.55 RPM	0.00 RPM
SRP007412_heart	7.18 RPM	0.00 RPM
SRP007412_kidney	9.22 RPM	0.00 RPM
SRP007412_liver	2.01 RPM	0.00 RPM
SRP007412_testis	6.29 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_290 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_290 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006017	1 retrocopy	retro_cfam_1658,
Choloepus hoffmanni	ENSCHOG00000007449	4 retrocopies	retro_chof_1039, retro_chof_2342, retro_chof_355, retro_chof_883,
Erinaceus europaeus	ENSEEUG00000002084	1 retrocopy	retro_eeur_254,
Monodelphis domestica	ENSMODG00000014543	1 retrocopy	retro_mdom_290 ,
Monodelphis domestica	ENSMODG00000018271	1 retrocopy	retro_mdom_25,
Otolemur garnettii	ENSOGAG00000013964	1 retrocopy	retro_ogar_2142,
Sorex araneus	ENSSARG00000014007	1 retrocopy	retro_sara_239,
Sarcophilus harrisii	ENSSHAG00000006597	2 retrocopies	retro_shar_485, retro_shar_56,