RetrogeneDB ID: retro_chof_1331

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_265163:90..1467(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RACGAP1
• Ensembl ID: ENSCHOG00000001701
• Aliases: None
• Description: Rac GTPase activating protein 1 [Source:HGNC Symbol;Acc:9804]

Sequence

>retro_chof_1331
GAAAAGCTGGAATGGCAGATTCAGCTGATTGAGAGATGCTCATGTGTGACACATCTGGCAGCATTCAACTAAGTGAAGAG
CAAAAATCAGCTTTGGCTTTTCTCAACAGGGGCCAAACATCCTGTGGCAGTGCTGGGAACAAAAGACTATCAACCATTGA
CAAATCTGGTTCCATTTTATCAGATACCAGCTTTGATGAGACTAATGAATCACTGGATTAGGGATTCTTCTTTGGTGAAG
ACTTTCAAACTGAAGAAGACAGAAAAGAGGCTCTCTAATAGCCGACAATTTATTGATGGTCCACCTGGATCTATAAAGAA
AACTCGTTCCATTGGCTCCATATCTGACCAGGGGAGTGAATCTATAGTTGCAAAGACTATGGTGACTTTTCCCAATGATG
GTGGGCCCATCGAAGCTGTGTCCATGATTGAGACTGTGCCATATTGGACCAGGAGCTGAAGGAAAACAGATACTTTACAA
CCTTGGAACAGTGACTCCACCCTCAGCAGCAAGCTGGAGCCCAGAACTGAGACAGACAGTCCCAGCACTCCACAGAGTAA
CAGAGGGATGTGCTTGCATGACTTTGTCTTTAAGACGGTTATTAAACCAGAATCTTGTGTTCCATGTGGAAAGCGGATAC
AATTTGGCAAGCTGTCCTTGAAGTGTCGAGACTGTCATGTGGTCTCTCATCCAGAATGTCAGAACTGCTGTCCCCTTCCC
TGCATTCCTACCCTGATAGGAACACCTGTCAAGATCAGAGAGGGAATGCTGGCAGATTTTGTGTCCCAGACTACATCAGT
GATCCCCTCCATTGTTGTCCACTATATAAATGAGATTGAACAGAGGGGTCTTACAGAGACAGGCCTGTATAGGATCTCAG
GCTGTGACCAGACAGCAAAAGAGTTGAAAGAGAAATTCCTCTGAGTGAAAACCGTGCTCCTCCTCAGCAAGGTGGATGAC
ATCCATGCTATCTGTAGCCTTCTGAAAGACTTCCTTCGAAACCTCAAAGAACCTCTTCTGAACTTTTGGCTAAATAAGGC
CTCTATGGAAGCAGCAGAAATCACAGATGAGGACAACAGCATAGCTGCCATGTACCAGGCTGTTGGTGATCTGCCCCAAG
TCAACAGGGACACATTAGCTTTCCTCATGATTCACTTGCAAAGAGTGGCTCAGAGCCTGAACACTAAAATGGATGTTGCC
AACCTGGCTAAAGTCCTTGGCCCTTAAATAGTTGCCCATGCTGGGCCCAATCCAGACCCAGTGGCAATGTTACAAGACAT
CAAGCATCAACTCAAGGTGGTGGAGTGCTTACTTTCACTGACTGTGGACTATTGGAGATAGTTCATGATGGTAGAGCAAC
AGAACATTGATCCCATA

Alignment

ORF - retro_chof_1331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.3 %
• Parental protein coverage: 72.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKLERQIQLIR-EMLMCDTSGSIQLSEEQKSALAFLNRGQPSNGNAGNKRLSTIDESGSILSDISFDKTD
          EKLE.QIQLI..EMLMCDTSGSIQLSEEQKSALAFLNRGQ.S.G.AGNKRLSTID.SGSILSD.SFD.T.
Retrocopy EKLEWQIQLIE<EMLMCDTSGSIQLSEEQKSALAFLNRGQTSCGSAGNKRLSTIDKSGSILSDTSFDETN

Parental  ESLD-WDSSLVKTFKLKKREKRRSNSRQFVDGPPGPIKKTRSIGSTADQGNESIVAKTTVTVPNDGGPIE
          ESLD..DSSLVKTFKLKK.EKR.SNSRQF.DGPPG.IKKTRSIGS..DQG.ESIVAKT.VT.PNDGGPIE
Retrocopy ESLD>RDSSLVKTFKLKKTEKRLSNSRQFIDGPPGSIKKTRSIGSISDQGSESIVAKTMVTFPNDGGPIE

Parental  AVSTIETVPYWTRSRRKTGTLQPCNSDSTLSSRRLEPRTETDSSSTPQSNGGMRLHDFVSKTVIKPESCV
          AVS.IETVPYWTRS.RKT.TLQP.NSDSTLSS..LEPRTETDS.STPQSN.GM.LHDFV.KTVIKPESCV
Retrocopy AVSMIETVPYWTRS*RKTDTLQPWNSDSTLSSK-LEPRTETDSPSTPQSNRGMCLHDFVFKTVIKPESCV

Parental  PCGKRIKFGKLSLKCRDCRVVSHPECRDRCPLPCIPTLIGTPVKIGEGMLADFVPQTSPMIPSIVVHCVN
          PCGKRI.FGKLSLKCRDC.VVSHPEC...CPLPCIPTLIGTPVKI.EGMLADFV.QT...IPSIVVH..N
Retrocopy PCGKRIQFGKLSLKCRDCHVVSHPECQNCCPLPCIPTLIGTPVKIREGMLADFVSQTTSVIPSIVVHYIN

Parental  EIEQRGLTETGLYRISGCDRTVKELKEKFLRVKTVPLLSKVDDIHAICSLLKDFLRNLKEPLLTFRLNKT
          EIEQRGLTETGLYRISGCD.T.KELKEKFL.VKTV.LLSKVDDIHAICSLLKDFLRNLKEPLL.F.LNK.
Retrocopy EIEQRGLTETGLYRISGCDQTAKELKEKFL*VKTVLLLSKVDDIHAICSLLKDFLRNLKEPLLNFWLNKA

Parental  FMEAAACL-HDDLYTALYLIDGDLSHLSIYIYPSIMIHLLSVAQSPNTKMDVANLAKVFGPTIVAHAVPN
          .MEAA.....D....A.Y...GDL...........MIHL..VAQS.NTKMDVANLAKV.GP.IVAHA.PN
Retrocopy SMEAAEITDEDNSIAAMYQAVGDLPQVNRDTLAFLMIHLQRVAQSLNTKMDVANLAKVLGP*IVAHAGPN

Parental  PDPVAMLQDIKRQPKVVERLLSLPLEYWSQFMMVEQENIDPM
          PDPVAMLQDIK.Q.KVVE.LLSL...YW..FMMVEQ.NIDP.
Retrocopy PDPVAMLQDIKHQLKVVECLLSLTVDYWR*FMMVEQQNIDPI

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_1331 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001701	1 retrocopy	retro_chof_1331 ,
Callithrix jacchus	ENSCJAG00000021058	2 retrocopies	retro_cjac_1325, retro_cjac_837,