RetrogeneDB ID: retro_chof_1503

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_310343:113..864(-)
• 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_1503
GGAATTGGTGGGGACCCTGCCCAATTGGCCCAGAACATCTCTTCCAACACCAAGAAGATCACACAATGTTCTGTGGAAAT
ACAAAAGCCTCTGAATCAACTTGGAGCACCCCAAGATTCTCCCAAATTGAGGCAACAGCTGCAACAGAAACAGCAGTATA
CTAACCATCTTGCCAATGAAACAAATAAACACATTAAAGAGTTTGGATTTCTTCTCACCACCCTCCAATGAACAGCAGCA
AAAGAAAATAAAGAAGGATTGCTTAGTGGCTGAATTCACAACCTCACTGACAAACTTTCAGAAGGTCCAGAGGCAAGTTG
CTGAGGGAAAAAGGAGTTTGTTGTTGAAGCAAGAGTCAGCTCCAAGGTATCTGGTGGTTTTCCAGATGAAGGGAATCTTG
TATCCTGGGAAAGCCAAACTCAACCTCAAGTGCATGTGCAGGATGAAGATATTACAGAGGATGACCTCTGCTTCATTCAT
GAGGCAGAGTCTTCTACTAGACAACACAAAGCTGATTATTATGGATATTAATGAAATATTTAAAGATTTAGGAATGATGA
TTTAAGAACAAGGAGATGTCACAGATAGCATAGAAGTCAATGTAGAAAATGCTGAGGTGCACATTCAACAAGGAAACCCG
CAGCTGTCAAGGGCAGCAGATTACCGGTGCAAATCCAGAAAAACTCTGTTCACCATCATTTTTATCCTTGTCATTGGATT
TGTGATTACTGGTCTCATCATATGGGGAGTG

Alignment

ORF - retro_chof_1503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.37 %
• Parental protein coverage: 97.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GIGGDPAQLAQRISSNIQKITQCSMEIQRTLNQLGTPQDSPELRQQLQQKQQYTNQLAKETDKLIKEFGS
          GIGGDPAQLAQ.ISSN..KITQCS.EIQ..LNQLG.PQDSP.LRQQLQQKQQYTN.LA.ET.K.IKEFG.
Retrocopy GIGGDPAQLAQNISSNTKKITQCSVEIQKPLNQLGAPQDSPKLRQQLQQKQQYTNHLANETNKHIKEFGF

Parental  LPTT-PSEQRQRKIQKDRLVAEFTTSLTNFQKVQRQAAE-REKEFVARVRASSRVSGGFPEDTSKERNLV
          L.TT...EQ.Q.KI.KD.LVAEFTTSLTNFQKVQRQ.AE...KEFV...R.SS.VSGGFP........LV
Retrocopy LLTT>SNEQQQKKIKKDCLVAEFTTSLTNFQKVQRQVAE<GKKEFVVEARVSSKVSGGFPDEGN----LV

Parental  SWESQTQPQVQVQDEEIMEDDLRLIQERESSIRQLEAD-IMDINEIFKDLGMMIHEQGEVIDSIEANTEN
          SWESQTQPQV.VQDE.I.EDDL..I.E.ESS.RQ..AD.IMDINEIFKDLGMMI.EQG.V.DSIE.N.EN
Retrocopy SWESQTQPQVHVQDEDITEDDLCFIHEAESSTRQHKAD>IMDINEIFKDLGMMI*EQGDVTDSIEVNVEN

Parental  AEMHVQPANQQLSRAAGYQRKSRKTLCIIIFSLGTG-VIISFIIWGV
          AE.H.Q..N.QLSRAA.Y..KSRKTL..IIF.L..G.VI...IIWGV
Retrocopy AEVHIQQGNPQLSRAADYRCKSRKTLFTIIFILVIGFVITGLIIWGV

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_1503 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 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,