RetrogeneDB ID: retro_mdom_697

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:151398476..151399011(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSMODG00000003107
• Aliases: None
• Description: serine/arginine-rich splicing factor 6 [Source:HGNC Symbol;Acc:10788]

Sequence

>retro_mdom_697
TCCTACATGAAGCATGCTATAAATAAATTGGATGGCACAGAAATAAATGACAAATATAAGATTAATTTAAGTTCAGCTAA
GGTAAAGCCATAGGAAATCTGTTCTCTGAGCAGATCTAGATCCCAGTCTAGGCAAATGTCTTAAAGTAGGATTTGAAGAA
GCAGCTAAAGTTGGTCCTGAAGTGCCTAAAAAGGTTGTTCGAGATCCAAATCTTGTGGTAAAGATCATTCATGATCCTGA
TCTGAAGGCAGAAAGTCTAGATCAAAGAGCAAATAAATCTAAGTCAACTGTGACTGAGGCTTTGGATCTCATAGCAGATC
TGAGGCAAAATCTGAAAAATAACACCATAGGTCCAGATTTACATCTCCCAAAGAAAATGGAAAAGGAGAAACAAAATCAA
AATTAAGATCAGGAAGCTAGTGTCACTTCACTTCATCACAAACTCCACCCCCATGAAAGACTCATTGTTGAGTCACTTTC
AGTCAGAAAATGCATCAGCATCAGTATTCTGTCACAATCAAGATCTAGTTCAAGA

Alignment

ORF - retro_mdom_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.19 %
• Parental protein coverage: 52.49 %
• Number of stop codons detected: 14
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDMKRALDKLDGTEINGR-NIRLIEDKPRTSHRRSYSGSRSRSRSRRRSRSRSRRSSRSRSRSASKSRSR
          S.MK.A..KLDGTEIN....I.L...K.......S.S.SR..S.SR..S.SR..RSS.S.S.SA.K..SR
Retrocopy SYMKHAINKLDGTEINDKYKINLSSAKVKP*EICSLSRSR--SQSRQMS*SRI*RSS*SWS*SA*KGCSR

Parental  SKSRSRSKDHSRSRSKGRKSRSKSK-SKAKSDRGSRSRSRSKAKSEKSRSRSRSPSPKENGKGETKSKSR
          SK..S..KDHS.S.S.GRKSRSKSK......D.G..S.SRS.AKSEK...RSR..SPKENGKGETKSK.R
Retrocopy SK--SCGKDHS*S*SEGRKSRSKSK*I*VNCD*GFGSHSRSEAKSEK*HHRSRFTSPKENGKGETKSKLR

Parental  SRSQSHSNSPQPPPPSKARS-ESPPVKRATSVS-HSRSRSRSR
          S.S..H..S.Q.PPP.K....ES..V....S.S..S.SRS.SR
Retrocopy SGS*CHFTSSQTPPP*KTHC>ESLSVRKCISISILSQSRSSSR

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	170.33 RPM
SRP007412_cerebellum	0.00 RPM	190.00 RPM
SRP007412_heart	0.00 RPM	147.52 RPM
SRP007412_kidney	0.00 RPM	294.97 RPM
SRP007412_liver	0.00 RPM	252.25 RPM
SRP007412_testis	0.00 RPM	183.27 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_697 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_697 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002061	1 retrocopy	retro_acar_191,
Canis familiaris	ENSCAFG00000009289	1 retrocopy	retro_cfam_392,
Echinops telfairi	ENSETEG00000006221	1 retrocopy	retro_etel_1261,
Homo sapiens	ENSG00000124193	1 retrocopy	retro_hsap_1809,
Gorilla gorilla	ENSGGOG00000009808	1 retrocopy	retro_ggor_2176,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697 ,
Monodelphis domestica	ENSMODG00000008669	1 retrocopy	retro_mdom_289,
Monodelphis domestica	ENSMODG00000011362	1 retrocopy	retro_mdom_934,
Nomascus leucogenys	ENSNLEG00000006524	1 retrocopy	retro_nleu_1294,
Oryctolagus cuniculus	ENSOCUG00000009785	1 retrocopy	retro_ocun_312,
Pongo abelii	ENSPPYG00000011019	1 retrocopy	retro_pabe_1483,
Pan troglodytes	ENSPTRG00000013506	1 retrocopy	retro_ptro_3057,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
Tupaia belangeri	ENSTBEG00000013448	1 retrocopy	retro_tbel_383,
Tursiops truncatus	ENSTTRG00000015410	2 retrocopies	retro_ttru_1786, retro_ttru_1787,