RetrogeneDB ID: retro_mdom_1005

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:189847967..189848693(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF12
• Ensembl ID: ENSMODG00000018282
• Aliases: None
• Description: serine/arginine-rich splicing factor 12 [Source:HGNC Symbol;Acc:21220]

Sequence

>retro_mdom_1005
ATGCCTCGATACACCAGGCCCCCCAACACCTCCCTTTTCGTCAGGAACGTCAGGGATACCACCAGACCTGAGGACTTGCA
ATGTGAATTTGGTCGATATGGCCCTATAGTAGACGTACACATTCCACTTGACTTCTACACTCGCTGCCCAAGAGGATTTG
CTTACTTACAATTTGAAGCTGTCTGTGATGCAGAAGATGCTCTTTATAACCTCAATAAAACGTGGGTATGTGGTCATCAA
ATTGAAATACAGTTTGCACAAGGTGATCGCAAAATACCAGGCCAAATGAAATCAAAAGAACGCCACCCTTGTTCTCCAAG
TGAACATAGAAGATCAAGAAGGCACAGTAGAAGGACTCGAAGTAGAAGTTCTTCATGGGGAAGAAGCCGGAGACAATCTG
ATAGCCTTAAAGAGTCTCCTCGTAGGGGACTTTCTTATAGCTGATCTAAATCTCGATCTAACTCATTAACAAGGCGTTCT
ACCTCAGGAAGGAAATCAAGATCTCCTAGAAGAAATTCTAGTTCTAGACGATGATCAAGATCTGAGTCCTTACAAAAAAG
GACCACATCTGTGGGAAAATCACAGTCAAGTTCACCTCAGAGGCAGACCATCTCAGGGGCAAAATCAAGATCAGGTGGAA
GACATTTTGATGTACTAGCAAGATCAAAATCTCACTAAAGACACACTAATTCTGAAACTAAAGCACAGTCTCAGAGCTAC
CATCAT

Alignment

ORF - retro_mdom_1005 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRYTRPPNTSLFVRNVTDATRPEDLRREFGRYGPIVDVYIPLDFYTRRPRGFAYLVIFEDVRDAEDALY
          M.RYTRPPNTSLFVRNV.D.TRPEDL..EFGRYGPIVDV.IPLDFYTR.PRGFAYL..FE.V.DAEDALY
Retrocopy MPRYTRPPNTSLFVRNVRDTTRPEDLQCEFGRYGPIVDVHIPLDFYTRCPRGFAYLQ-FEAVCDAEDALY

Parental  NLNKKWVCGRQIEIQFAQGDRKTPGQMKSKERHPCSPSEHRRSRSHSRRTRSRSSSWGRSRRRSDSLKES
          NLNK.WVCG.QIEIQFAQGDRK.PGQMKSKERHPCSPSEHRRSR.HSRRTRSRSSSWGRSRR.SDSLKES
Retrocopy NLNKTWVCGHQIEIQFAQGDRKIPGQMKSKERHPCSPSEHRRSRRHSRRTRSRSSSWGRSRRQSDSLKES

Parental  RRRGLSYSRSKSRSNSLTRHSTSGRKSRSPRRNSSSRRRSRSESLQKRTTSVGKSQSSSPQRQTTSGAKS
          .RRGLSYS.SKSRSNSLTR.STSGRKSRSPRRNSSSRR.SRSESLQKRTTSVGKSQSSSPQRQT.SGAKS
Retrocopy PRRGLSYS*SKSRSNSLTRRSTSGRKSRSPRRNSSSRR*SRSESLQKRTTSVGKSQSSSPQRQTISGAKS

Parental  RSGGRHFDSLARSPSKSPQRHTNSETKAQSRSYHH
          RSGGRHFD.LAR..SKS..RHTNSETKAQS.SYHH
Retrocopy RSGGRHFDVLAR--SKSH*RHTNSETKAQSQSYHH

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_1005 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1005 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000014941	1 retrocopy	retro_mmul_100,
Monodelphis domestica	ENSMODG00000018282	1 retrocopy	retro_mdom_1005 ,
Tupaia belangeri	ENSTBEG00000015120	1 retrocopy	retro_tbel_31,