RetrogeneDB ID: retro_mdom_146

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:114013041..114013656(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024936
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008253
• Aliases: None
• Description: None

Sequence

>retro_mdom_146
ATGGAAGAGGATGTGCTGACCACCCTGAAGATCCTGATCATTGGGGAAAGTGGGGTGGGCAAATCCAGTCTTCTGTTGAG
AATCACAGATGATACCTTTGATCCAAATATTTCAGCAACAATTGGTGTTGATTTCAAGGTTAAAACTATATCGTTTGATG
GAAATAAAGCCAAGCTTGCAATATGGGATACTGCAGGTCAGGAGCGCTTCAGAACACTGACGCCTAACTATTACAGAGGT
GCACAGGGTGTTATATTAGTTTATGATGTCACAAGAAGAGATACTTTTGTTAAGCTGGATAACTGGTTAATTGAATTGAA
TACACATTGCATGGGAAATGACATAACAAAAATGCTAGTTGGAAACAAAATTGATAAGGAAAACCATGAAGTTGATAGAA
ATGAAGGACTGAAATTTGCACGGAAGCATTCCATGTTATTTATAGAGGTTAGTGCAAAAACTTGTGATGGTGTACGATGT
GCCTTTGAAGAACTTGTTGAAAAGATCTTTCAAACACCTGGAGTATGGGAGATTAAGAACCAGAAAAAAGGAGTAAGGCT
ATCACAGAATGAAGAAAGTCCTGGAAGAGTTTGTGGAGGATGTTTTTCTATGCTA

Alignment

ORF - retro_mdom_146 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDEDVLTTLKILIIGESGVGKSSLLLRFTDDTFDPELAATIGVDFKVKTISVDGNKAKLAIWDTAGQERF
          M.EDVLTTLKILIIGESGVGKSSLLLR.TDDTFDP...ATIGVDFKVKTIS.DGNKAKLAIWDTAGQERF
Retrocopy MEEDVLTTLKILIIGESGVGKSSLLLRITDDTFDPNISATIGVDFKVKTISFDGNKAKLAIWDTAGQERF

Parental  RTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLSELETYCTRNDIVKMLVGNKIDKENREVDRNEGLKFA
          RTLTP.YYRGAQGVILVYDVTRRDTFVKLDNWL.EL.T.C..NDI.KMLVGNKIDKEN.EVDRNEGLKFA
Retrocopy RTLTPNYYRGAQGVILVYDVTRRDTFVKLDNWLIELNTHCMGNDITKMLVGNKIDKENHEVDRNEGLKFA

Parental  RKHSMLFIEASAKTCDGVQCAFEELVEKIIQTPGLWESENQNKGVRLSHREESHGGACGGYCSML
          RKHSMLFIE.SAKTCDGV.CAFEELVEKI.QTPG.WE..NQ.KGVRLS..EES.G..CGG..SML
Retrocopy RKHSMLFIEVSAKTCDGVRCAFEELVEKIFQTPGVWEIKNQKKGVRLSQNEESPGRVCGGCFSML

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_146 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_146 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009871	1 retrocopy	retro_btau_1691,
Choloepus hoffmanni	ENSCHOG00000005565	4 retrocopies	retro_chof_2391, retro_chof_256, retro_chof_396, retro_chof_846,
Cavia porcellus	ENSCPOG00000002234	2 retrocopies	retro_cpor_633, retro_cpor_652,
Dipodomys ordii	ENSDORG00000014338	1 retrocopy	retro_dord_419,
Monodelphis domestica	ENSMODG00000008253	1 retrocopy	retro_mdom_146 ,
Oryctolagus cuniculus	ENSOCUG00000022307	2 retrocopies	retro_ocun_1699, retro_ocun_841,
Otolemur garnettii	ENSOGAG00000028015	2 retrocopies	retro_ogar_2587, retro_ogar_2973,
Rattus norvegicus	ENSRNOG00000018972	2 retrocopies	retro_rnor_2744, retro_rnor_2962,
Sarcophilus harrisii	ENSSHAG00000007613	1 retrocopy	retro_shar_281,