RetrogeneDB ID: retro_chof_1245

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_235861:618..1473(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCE1
• Ensembl ID: ENSCHOG00000008727
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109]

Sequence

>retro_chof_1245
AAGTACAATGGATCTTTGAAGGCCTATCACAATTCCCCTGCATACCTTGCTTATATAAATGCAAAAAGTCATGCAGAAGC
TGCTCTAGAGGAGGAAAGTCAACAGAAACAGTCTTGCATGGAGAAAGGAGAACCTTACTTGAGCATTCAGCCTGCTGAAG
ATCCAGATGATTATGATGATGGCTTTTCAATGAAGCATACAGCCTCCACCCATTTCTAGAGATATCACTGCCTCATCAGT
GAAATCCTTAGTAAGAGTGTGGTGCCAGATGTTTGGTCAGTTGTCACAACAGCTAGAATGCAGGTCCTCAAACAACAGGT
CCAGTCCTTAATCATTCATCAGTTAAAACTAGAAGCTGAACTTCTTCAAATAGAGGAGTGACACTAGAAAAAAGAAGAGG
AAATTCCTGGAAAACACAGAATCATTTAACAATGAACTTTAAAGTTTGCATGGTTTGAAGGTAGAAGTGTACTTGCAAAA
ATTTGCAGGTGAAATTGCACAGGCAAAGGAACAGACCCACAAAAGGCAAGAGGAAAGGGAGAAAGAGGCAGCAGAACAAG
CTGAACACAGCCAGAGCAATATTGTTCCTGAAGAAGAGCAGGCAGCTAATAAAATCAAAGAAAAAGGAAAATGAGAGCAC
TCCAGTGGAGACAGAGGAGGCACATCTTGAAGAAACAAGAGAAGTACAACAGAATGGTGAAGAAGGCACAGTTACTGAGG
ACAAGGAGAGTGGGCAGGAGGGGGTTGACAGTATGGAAGGAAGGAACCAATGATAGCAACACTGGCTTAGAGAGCAATAG
TGCAACAGTGGAGGAGCAACAAACAGATCCCATATCAAAAGAGGAGAAAAAAGAA

Alignment

ORF - retro_chof_1245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.09 %
• Parental protein coverage: 69.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EYNESMKAYHNSPAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYDDGFSMKHTATA
          .YN.S.KAYHNSPAYLAYINAKS.AEAALEEES.Q.QS.MEKGEPY.SIQPAEDPDDYDDGFSMKHTA..
Retrocopy KYNGSLKAYHNSPAYLAYINAKSHAEAALEEESQQKQSCMEKGEPYLSIQPAEDPDDYDDGFSMKHTAST

Parental  RFQRNHRLISEILSESVVPDRRSV-TTARMQ-LKRQVQSLM-HQRKLEAELLQIEERH-QEKKRKFLEST
          .F.R.H.LISEILS.SVVPD..SV.TTARMQ.LK.QVQSL..HQ.KLEAELLQIEE.H...KKRKFLE.T
Retrocopy HF*RYHCLISEILSKSVVPDVWSVVTTARMQVLKQQVQSLIIHQLKLEAELLQIEE*H>RKKKRKFLENT

Parental  DSFNNELKRLCGLKVEVDMEKIAAEIAQAEEQARKRQEEREKEAAEQAEHSQSSIVPEEEQVANKI-EEK
          .SFNNEL..L.GLKVEV...K.A.EIAQA.EQ..KRQEEREKEAAEQAEHSQS.IVP.EE..A......K
Retrocopy ESFNNEL*SLHGLKVEVYLQKFAGEIAQAKEQTHKRQEEREKEAAEQAEHSQSNIVP-EEEQAANK>SKK

Parental  KEDESIPMETEEAHLEETTEGQQNGEEGTSTEDKES-GQEGVDSMAEEGTSDSNTGSDSNSATVEETPTD
          KE.ES.P.ETEEAHLEET.E.QQNGEEGT.TEDKES.G..G......EGT.DSNTG..SNSATVEE..TD
Retrocopy KENESTPVETEEAHLEETREVQQNGEEGTVTEDKES>GRRGL-TVWKEGTNDSNTGLESNSATVEEQQTD

Parental  PIPEEEKKE
          PI..EEKKE
Retrocopy PISKEEKKE

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_1245 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 11 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016025	8 retrocopies	retro_cfam_1057, retro_cfam_1131, retro_cfam_1134, retro_cfam_1300, retro_cfam_1412, retro_cfam_1803, retro_cfam_2063, retro_cfam_2127,
Choloepus hoffmanni	ENSCHOG00000008727	3 retrocopies	retro_chof_1245 , retro_chof_482, retro_chof_573,
Callithrix jacchus	ENSCJAG00000013573	4 retrocopies	retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Felis catus	ENSFCAG00000009646	2 retrocopies	retro_fcat_234, retro_fcat_513,
Gorilla gorilla	ENSGGOG00000011803	2 retrocopies	retro_ggor_1020, retro_ggor_931,
Macaca mulatta	ENSMMUG00000004005	3 retrocopies	retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furo	ENSMPUG00000014660	4 retrocopies	retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Oryctolagus cuniculus	ENSOCUG00000008981	1 retrocopy	retro_ocun_59,
Pongo abelii	ENSPPYG00000008456	4 retrocopies	retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Rattus norvegicus	ENSRNOG00000010676	7 retrocopies	retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tursiops truncatus	ENSTTRG00000013885	1 retrocopy	retro_ttru_1217,