RetrogeneDB ID: retro_tbel_383

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1915:34851..35377(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF6
• Ensembl ID: ENSTBEG00000013448
• Aliases: None
• Description: serine/arginine-rich splicing factor 6 [Source:HGNC Symbol;Acc:10788]

Sequence

>retro_tbel_383
GAAATAAATAGAAGGAATATTACGCTTGTTGAAGATAAGCCACGAGGAAGTCATAGATGATCTTATTTTGGAAGCATTTC
CAAGTCACAGTCTCGAAGAAGGTCATGAAGTAGGAGTCACAGGAGCAGCAGCAGTAGATTTCGAAGTATCTCAAAAAGTT
GCTCCCTATTCAGGTCGTGGAGCAAAGGTCGCTCACGTTCTTGACCAAAATGAAGTAAATTTGGATCAAAAAGCAAATCC
AAGGCCAAGTCCCATTGGCGCTCCTGTTCACATTCTGAAAGCAGATCTAAGGATGAGTGTGAGAAATCTCAAAGCAGGTT
TTGATCTCAATTCCCCCAATGAAAATGGAAAAGGTGATATAAAGTCAAAATGCAGGTCAAGTATCCAATCTTGTTCAAAT
TCACCCCTACCTGTTCTACCCTCAAAGGCTCGTTCTGTGTCCCCTCCACCAAAAAGAGCTACTTCAAGGTCCCATTCTAG
ATCTCGCTCAAAGTCAAGATCAAGGTCCAGCTCGAATTCCACAGAT

Alignment

ORF - retro_tbel_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 55.91 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EINGRNIRLIEDKPRGSHRRSYSGSRSRSRSRRRSRSRSRRSSRSRSRSISKSRSRSRSRSKGRSRSRSK
          EIN.RNI.L.EDKPRGSHR.SY.GS.S.S.SRRRS.SRS.RSS.SR.RSISKS.S..RS.SKGRSRS..K
Retrocopy EINRRNITLVEDKPRGSHR*SYFGSISKSQSRRRS*SRSHRSSSSRFRSISKSCSLFRSWSKGRSRS*PK

Parental  GRKSRSKSKSKAKSDRGSRSRSRSRSKDEYEKSRSRSRSR-SPKENGKGDIKSKSRSRSQSRSNSPLPVP
          ..K..SKSKSKAKS...S.S.S.SRSKDE.EKS.SR..S..SP.ENGKGDIKSK.RS..QS.SNSPLPV.
Retrocopy *SKFGSKSKSKAKSHWRSCSHSESRSKDECEKSQSRF*SQ>SPNENGKGDIKSKCRSSIQSCSNSPLPVL

Parental  PSKARSVSPPPKRATSRSRSRSRSKSRSRSRSSSRD
          PSKARSVSPPPKRATSRS.SRSRSKSRSRS.S.S.D
Retrocopy PSKARSVSPPPKRATSRSHSRSRSKSRSRSSSNSTD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_383 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_383 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002061	1 retrocopy	retro_acar_191,
Canis familiaris	ENSCAFG00000009289	1 retrocopy	retro_cfam_392,
Gorilla gorilla	ENSGGOG00000009808	1 retrocopy	retro_ggor_2176,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697,
Oryctolagus cuniculus	ENSOCUG00000009785	1 retrocopy	retro_ocun_312,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752,
Tupaia belangeri	ENSTBEG00000001972	1 retrocopy	retro_tbel_2707,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tupaia belangeri	ENSTBEG00000013448	1 retrocopy	retro_tbel_383 ,