RetrogeneDB ID: retro_chof_1058

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_19128:965..1997(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF4
• Ensembl ID: ENSCHOG00000013858
• Aliases: None
• Description: serine/arginine-rich splicing factor 4 [Source:HGNC Symbol;Acc:10786]

Sequence

>retro_chof_1058
TATGGTTTTGTGGAGTCAGATGATCTCCCATATGCAGAAGGATGCTGTTTATGAACTAAATGGCAGGAAACATTTGTGGT
CAGGAGTCATCATTGAGCAAGCCGGTAGACCATGTCAAGATGGCAGTTAGGGTTCTGGATGCAGTGGATATAGTTATAGA
AGAAGTAGTCGAAATAAATATGGCCCTCCTACCTGCACTGACAGACTTACGGTGGAAAATTTGTCAAGTCGGTGCAGCTG
GCATGACCTAAAGGATTATGTGCATCAGGCAGAAGTGACCTATGCAGATGATCATAAGGGGTGCAGAAAATGAAGGACTG
ATTGAATTTGTGTCTTATTCTGATGTGAAAAGCATTTTGGAAAAGTTGTATGGAGCTGAAGTCAATGGAAGAAAAAATCA
GATTAGTGGAAGGCAAGCTGGCTCTCCATGATGCGGGTCCTACTCCAGGAGCTGGAGTCACTCAAGATCTCGCTCTTGAA
GCAGACATTCCCATGAGAGTTGCAGCTGATGTGGCAGCAGCAAAAGCAGTCATTCTAAGAGTAGATCCCAATCCAGGTCG
GGCTCCCATTCCTGGGGCAAGAGGCAGAGCCAGAGCCAGAGCTGGAGCAAGAAGGAGAAAAGCAGGAGCCCCAGCAAGGA
TGATGACAGCCGCAGCAAGGGTACAGACGACACCAGGGAGAGGATCCAGAACAGCAACAGTGTTGGGAAATCCCAGAGCC
AGAGTCCCAGTAGGCATAAAAGTAAGAGTAAAAGTAGAAGCAGGAGTCAAGAGAGGAGAGTGAAGGAGGAGAAGTGAGGG
ACTGCGAGCAGTAGAAGCAAGGAGAAGAGCAGGAGTCAGGAGAAAAACTTCCTCAAGAGTAGGAGCAGAAGTAGGAGCCG
GAGCAGGAGCCACAGCCCTGTCAAAAGAGAGAAGACAGCCCAGCAGCAAGCGAGATAGCATGTCAGGCAATAACAAGAAG
AAGGAAGACACCCACTGCTCCCAGTCCAGATCGCAATCCTGCTCATGTCAAAGGAGCAGGAACACACCAAGT

Alignment

ORF - retro_chof_1058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.46 %
• Parental protein coverage: 77.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YGFVEFDDQQDAD-DAVYELNGKDLCGERIIVEHTCGPRRDGSYSFGCSGYGYRRSGRDKYGPPTRTEYR
          YGFVE.DD...A..DAVYELNG........I.E....P..DGS...GCSGY.YRRS.R.KYGPPT.T..R
Retrocopy YGFVESDDLPYAE>DAVYELNGRKHLWSGVIIEQAGRPCQDGS*GSGCSGYSYRRSSRNKYGPPTCTD-R

Parental  LIVENLSSRCSWQDLKDYMRQAGEVTYADAHKG-RKNEGVIEFVSYSDMKRALEKLDGTEVNGRK-IRLV
          L.VENLSSRCSW.DLKDY..QA.EVTYAD.HKG...NEG.IEFVSYSD.K..LEKL.G.EVNGRK.IRLV
Retrocopy LTVENLSSRCSWHDLKDYVHQA-EVTYADDHKG>AENEGLIEFVSYSDVKSILEKLYGAEVNGRK>IRLV

Parental  EDK-PGSRRRRSYSRSRSHSRSRSRSRHSRKSRSRSGSSKSSHSKSRSRSRSGSHSRSKSRSRSQSRSRS
          E.K..GS....SYSRS.SHSRSRS.SRHS..S.S..GSSKSSHSKSRS.SRSGSHS..K....SQS.S.S
Retrocopy EGK<AGSP*CGSYSRSWSHSRSRS*SRHSHESCS*CGSSKSSHSKSRSQSRSGSHSWGK--RQSQSQSWS

Parental  KKEKSRSPSKDDKSRSRSRSADKSHSKSKDQAEEKIQNNDSAGKSKSQSPSRHKSKSKSRSRSQERRVEE
          KKEKSRSPSKDD.SRS........................S..KSKS.S.....S.S..R....E.....
Retrocopy KKEKSRSPSKDDDSRSKGTDDTRERIQNSNSVGKSQSQSPSRHKSKSKS----RSRSQERRVKEEK*GTA

Parental  EKGSVTRSRSQEKNPLKSRSRIRSRSKGGS-RSQSQSHSKSK-DKRKGRKRSREESH-SQSHIHSKS-ER
          ...S...SRSQEKN.LKSRSR.RSRS...S..S.......SK.D...G.....E..H.SQS...S.S..R
Retrocopy SSRSKEKSRSQEKNFLKSRSRSRSRSRSHS>LSKERRQPSSKRDSMSGNNKKKEDTHCSQSRSQSCSCQR

Parental  SRKQGS
          SR...S
Retrocopy SRNTPS

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1058 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Choloepus hoffmanni	ENSCHOG00000013858	1 retrocopy	retro_chof_1058 ,
Callithrix jacchus	ENSCJAG00000009971	3 retrocopies	retro_cjac_3688, retro_cjac_3883, retro_cjac_3899,
Microcebus murinus	ENSMICG00000008965	1 retrocopy	retro_mmur_1597,
Otolemur garnettii	ENSOGAG00000015515	1 retrocopy	retro_ogar_2205,