RetrogeneDB ID: retro_chof_2631

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_92581:1851..2554(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STX7
• Ensembl ID: ENSCHOG00000010117
• Aliases: None
• Description: syntaxin 7 [Source:HGNC Symbol;Acc:11442]

Sequence

>retro_chof_2631
ATGTCTCACCCTCCGGGAATTGGTGGCGACCCTGCCCGGTGGCCCAGGCCATCTCTTCCAACACCCAGAGATCACACACT
GTTGTAATACAAAGGACCCCGAATCAACGTGGAACACCCCAAGCTTCTCCCAAGTTGACGCAACAGCTGTCACAGAAGCA
GAAGTGCATAAACTAACTTGCCAAAGAAACAGAAACATGCACGGAATAGTTGGGTCTCTTCCCAGCCAGCCAACAGTGGC
AAAGTAAAAGACAGACGGAGAACTCCGTGGCTGAATTCACAACCTCACTGATGAGCTTGCAGAAGGTCCAGAGGCCACCT
AATGAAAGAGAGGAGGAGTCCGTTGCTCGAGAAAGAGCCAGCTCCAGAGTATCTGGTGGTTTTCCAGGAGACAGTCCAAA
AGAAAGGAATCTTGTATCCTGGGAAATCCAAACTCAACCTCAAGTGCAAGTGCCAGATGAAGAAATTACAGAGGATCACT
CCACCTCATTCACGAGAGAGGGTCTTCTATTAGGCAACTTGAAGCTGATATTACGGATATTAGTGCAATATTTAAAGATT
TGGGAATGATGATTCATCAACAAGGAGATGCGATAGATAGCACAGAAGCCAATGTAGAAAACTCTGAGGTGCCCGTTCAA
CAAGCAAACCAACAGCTATCAGGAGCAGCAGCTTACCAGTGCAAATCCAGAAAAACCCTGTGT

Alignment

ORF - retro_chof_2631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.8 %
• Parental protein coverage: 91.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSYTPGIGGDPAQ-LAQRISSNIQKITQCSMEIQRTLNQLGTPQDSPELRQQLQQKQQYTNQLAKETDKL
          MS..PGIGGDPA...AQ.ISSN.Q........IQRT.NQ.GTPQ.SP.L.QQL.QKQ...N.LAKET...
Retrocopy MSHPPGIGGDPAR<VAQAISSNTQR--SHTVVIQRTPNQRGTPQASPKLTQQLSQKQKCIN*LAKETETC

Parental  IKEFGSLPTTPSEQRQRKIQKDRLVAEFTTSLTNFQKVQRQAAEREKEFVARVRASSRVSGGFPEDTSKE
          ....G..P...S.Q.Q.K.Q....VAEFTTSL...QKVQR...ERE.E.VAR.RASSRVSGGFP.D..KE
Retrocopy TE*LGLFPA--SQQWQSKRQTENSVAEFTTSLMSLQKVQRPPNEREEESVARERASSRVSGGFPGDSPKE

Parental  RNLVSWESQTQPQVQVQDEEIMED-DLRLIQERESSIRQLEADIMDINEIFKDLGMMIHEQGEVIDSIEA
          RNLVSWE.QTQPQVQV.DEEI.ED..L.LI.ER.SSIRQLEADI.DI..IFKDLGMMIH.QG..IDS.EA
Retrocopy RNLVSWEIQTQPQVQVPDEEITED<SLHLIHERGSSIRQLEADITDISAIFKDLGMMIHQQGDAIDSTEA

Parental  NTENAEMHVQPANQQLSRAAGYQRKSRKTLC
          N.EN.E..VQ.ANQQLS.AA.YQ.KSRKTLC
Retrocopy NVENSEVPVQQANQQLSGAAAYQCKSRKTLC

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_2631 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010117	3 retrocopies	retro_chof_1503, retro_chof_2631 , retro_chof_829,
Dasypus novemcinctus	ENSDNOG00000000295	1 retrocopy	retro_dnov_600,
Felis catus	ENSFCAG00000002292	1 retrocopy	retro_fcat_977,
Myotis lucifugus	ENSMLUG00000004301	1 retrocopy	retro_mluc_494,
Sarcophilus harrisii	ENSSHAG00000014440	1 retrocopy	retro_shar_430,
Tursiops truncatus	ENSTTRG00000009853	1 retrocopy	retro_ttru_185,