RetrogeneDB ID: retro_mdom_1197

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:444668878..444669525(-)
• Located in intron of: ENSMODG00000001959

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018439
• Aliases: None
• Description: None

Sequence

>retro_mdom_1197
GCCACTCCAGGTCGCTGGTTTCAGCACCATGCCCTCTGCTGGGGATAGGAGCTTCAGAGTAGCCCTGGAAGGAGCTACGC
AGCCAGCTTTGCTCAGACCTCTCCACCATTTGGATTCCTCTTTGACATTAATGGTGTTTTTATCCATGGCCACAGAGTGA
TCCCTGCTGCCTTGGAAGCTGCCCAAAAGCTGGTTGACTCACATGAGCATTTCCAAATGCCGGTTGTCTTTGTCACTAAT
GCTGGAAATTGTGCACCAAATGTAAAAGCTCAGGAATTGTCAGACCTTCTGGGTCTGAAGGTTGACCCAGAACAAGTAAT
ACTTTCCACCAGTCCCTTGAAATTCTTCTCAAAGTTCCATAATAAGTGAATGCTGGTATGGGGCAGGGGCCTATGATGGG
CAATGCCCAGAACTTGGGCTTCCAGAATGTGGTTACTATTGATGAATTGAGATCTGCATTTCCTCTGCTTGACATGGTTG
ATCTTGAACAATGGCCAAAGACTATGCCTCCCTTGACATCTGCCCTCCCCCCCCTCCCAATAGAAGGGGTACTTCTCTTC
AGAGAGCTAGTCAGCTAGGAGACAAGTCTCCAGCTCATCATGGATGTCCTCAGCAATAGGAACCCTGGCACAGGGCTGCT
AGTAGCC

Alignment

ORF - retro_mdom_1197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.73 %
• Parental protein coverage: 58.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAPGRWLRHRALCRGWELQGSPGRSYAAGLAQTSPTFGFLFDIDGVFIRGHKVIPAALEAARKLVDSHGH
          A.PGRW..H.ALC.G.ELQ.SPGRSYAA..AQTSP.FGFLFDI.GVFI.GH.VIPAALEAA.KLVDSH.H
Retrocopy ATPGRWFQHHALCWG*ELQSSPGRSYAASFAQTSPPFGFLFDINGVFIHGHRVIPAALEAAQKLVDSHEH

Parental  FRMPVVFVTNAGNCAPHVKAQELSDLLGLQVDPEQVILSSSPLKFFSKFHNKRMLV-SGQGPMVDNARNL
          F.MPVVFVTNAGNCAP.VKAQELSDLLGL.VDPEQVILS.SPLKFFSKFHNK.MLV..GQGPM..NA.NL
Retrocopy FQMPVVFVTNAGNCAPNVKAQELSDLLGLKVDPEQVILSTSPLKFFSKFHNK*MLV<MGQGPMMGNAQNL

Parental  GFQNVVTIEELRSAFPVLDMVDLERRPKTMPPLTS--DFPPIEGVLLFGEPVRWETNLQLIMDVLLSNGN
          GFQNVVTI.ELRSAFP.LDMVDLE..PKTMPPLTS.....PIEGVLLF.E.V..ET.LQLIMDV.LSN.N
Retrocopy GFQNVVTIDELRSAFPLLDMVDLEQWPKTMPPLTSAXXXXPIEGVLLFRELVS*ETSLQLIMDV-LSNRN

Parental  PGTGLAVA
          PGTGL.VA
Retrocopy PGTGLLVA

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_1197 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1197 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000018439	1 retrocopy	retro_mdom_1197 ,
Otolemur garnettii	ENSOGAG00000009307	1 retrocopy	retro_ogar_1316,