RetrogeneDB ID: retro_mdom_924

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:461404153..461405043(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020112
• Aliases: None
• Description: None

Sequence

>retro_mdom_924
ATGGCCACACTGGCGTTGCTGCTGGCACTGCTGTACGTGATTCCATGACTTTCGCGATGGCTGGCCAGGCCCTACTGCCT
CTTCTCAGCACTGCTACTGGTCTCCTTCCTGCTCGTGAGGAAGCTGCCACCGCTGTTCCTCGGTCTCCCCACACAGCGCG
AGGATGGCAATTCCTGCGACTTTGACTGGAGGGAGGTGGATATCTTAATGTTCCTCAGTGCCATTGTAATGATGAAGAAC
CGGAGATCAATCACTGTGGAGCAGCATGTAGGTAACATCTTCATGTTCAGTAAAGTGGCGAACACCATCCTCTTTTTCCA
CCTGGACATCCGCATGGGGCTTCTCTAAATCACACTCTGCATAGTGTTCCTGACGACTTGCAAACCCCCTCTCTACATGG
GCCCAGAATACATCAAGTACTTTTTTAATGACAAGACAATCGATGAAGAGCTGGAATGGACAACTAGATCACATGGATTG
TTGAGTTTTTTGCCAATTGGTCTAATAAGTGCCAGTCATTTGCTCTTATCTACTCTGACTTCTCCCTCAAGTATAATTGT
ACAGGGTTGAATTTTGGGAAAGTGGATGTTGGACGCTACCCTGATGTCAGTACACGATATAAACTGAGCACATCACCTCT
CACCAAGCAGCTTCCAACCCTGATCCTATTTCAGGGGGGCAAAGAGGTCATGAGAAGACCCCAGATTGACAAGAAGGGTT
GAGCTGTCTCTTGGACATTCTCTGAAGAGAATGTGATCCGAGAGTTCAGCCTGAATGAGTTGTATCAACGTGCCAAGAAG
CAGAACAAGTCCCGGGATGAGATTCCTGAGGAGCAACCTGAATCTGCAGCCCCTCACACACAGCCTGATGAGGAGAACAA
GAAGGACAAA

Alignment

ORF - retro_mdom_924 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVLAPLLALLYSIPRLSRWLARPYCLLSALLSASFLLVRKLPPLCLGLPTQREDGNSCDFDWREVEILM
          MA.LA.LLALLY.IP.LSRWLARPYCL.SALL..SFLLVRKLPPL.LGLPTQREDGNSCDFDWREV.ILM
Retrocopy MATLALLLALLYVIP*LSRWLARPYCLFSALLLVSFLLVRKLPPLFLGLPTQREDGNSCDFDWREVDILM

Parental  FLSAIVMMKNRRSITVEQHVGNIFMFSKVANTILFFRLDIRMGLLYITLCIVFLMTCKPPLYMGPEYIKY
          FLSAIVMMKNRRSITVEQHVGNIFMFSKVANTILFF.LDIRMGLL.ITLCIVFL.TCKPPLYMGPEYIKY
Retrocopy FLSAIVMMKNRRSITVEQHVGNIFMFSKVANTILFFHLDIRMGLL*ITLCIVFLTTCKPPLYMGPEYIKY

Parental  F-NDKTIDEELE-RDKRITWIVEFFANWSNECQSFAPIYADLSLKYNCTGLNFGKVDVGRYPDVSTRYKV
          F.NDKTIDEELE..D..ITWIVEFFANWSN.CQSFA.IY.D.SLKYNCTGLNFGKVDVGRYPDVSTRYK.
Retrocopy FFNDKTIDEELE<MDN*ITWIVEFFANWSNKCQSFALIYSDFSLKYNCTGLNFGKVDVGRYPDVSTRYKL

Parental  STSPLTKQLPTLILFQGGKEVMRRPQIDKKGRAVSWTFSEENVIREFSLNELYQRAKKQNKSRDVIPEEQ
          STSPLTKQLPTLILFQGGKEVMRRPQIDKKG.AVSWTFSEENVIREFSLNELYQRAKKQNKSRD.IPEEQ
Retrocopy STSPLTKQLPTLILFQGGKEVMRRPQIDKKG*AVSWTFSEENVIREFSLNELYQRAKKQNKSRDEIPEEQ

Parental  PESTAPQTQPDEENKKDK
          PES.AP.TQPDEENKKDK
Retrocopy PESAAPHTQPDEENKKDK

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_924 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_924 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
Callithrix jacchus	ENSCJAG00000035426	1 retrocopy	retro_cjac_3263,
Homo sapiens	ENSG00000213593	1 retrocopy	retro_hsap_4158,
Gorilla gorilla	ENSGGOG00000001519	1 retrocopy	retro_ggor_2792,
Monodelphis domestica	ENSMODG00000020112	1 retrocopy	retro_mdom_924 ,
Mus musculus	ENSMUSG00000050043	1 retrocopy	retro_mmus_154,
Pan troglodytes	ENSPTRG00000033702	1 retrocopy	retro_ptro_2827,