RetrogeneDB ID: retro_chof_1782

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_382587:25..1096(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1GALT1
• Ensembl ID: ENSCHOG00000000225
• Aliases: None
• Description: core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 [Source:HGNC Symbol;Acc:24337]

Sequence

>retro_chof_1782
TGGCTGAATTTTTTAATCTTCCTCCATGGATCAGCAATCGGATTTTTTTTTTTTTAATGTTCTCAGCTATTTAGTATTTT
GTTGGAAGAACGAGTGATACCCAAGCTAATACTTTTCATAATGATCCTCATGCTAGACATGCAGATGGTAACAGACAGAA
TCATCTAGAAGGACAAATGAACTTCAGTGCTGATGTTAGCCAACATAAAGATGACGACACAGACCTCGCTGAAAAACTCT
ACCAGAAGATTAAAATTCTTTGCTGGGTTATGACAGGACCTCAAAATTCAGAGAAAAAGGCCAAACATGTCAAAGCTACA
TGGACCCAATGTTGTAATGAAGTTCTGTTTATGAGTTCAGAAGAAAATAAAGACTTCCCTACTGTGGGATTAAAAACCAA
AGGCAGAGAGCAACTATACTGGAAAACAATTAAAGCTTTTCAGTATGTTTATGACCATTATTTAGAAGATGGTGATTGGT
TACGAAAGCAGATGATGATACACATTTCATACGAGACAACTTGAGATGCCTTCTTTCAAAATATGACCCTGAAAAACCCA
TTTACTTTGGGAGAAGATTTAAGCCCTACGTAAAGCAGGCCTACATGAGTGGAGGAGCAGGCTGTGTATTGAGCAAGGAA
GCCCTGAAGAGATTTGTTGATGCATTTAAAGCAAAGAAATGTACACACAGTTCCTCCATCAAAGATTTAGCACTGGAAGA
TGCATGGAAATTACAGATGTAGAAGCAGGAGATTCCAGAGATACCACTGGGAAAGAAACCTTTCATCCCTGTGTACCAGA
ACACCACTTAATCAAAGGTTATCTATCCAAAACATTTTGGTACTGGGATTATAACTATCATTCTCCTGTAGAGGGTCCTG
GATGCTATTCTGACCTCGCAATTTCTTTTCATTATATTGACCCGCTACCTACGTATGAGTTAGAATACCTCATTTATCAT
CTTCACCCATATGGTTATTTACACAGATATCAACCTGCCTTACCTGAGAATATACTAAAGAAAATAAGTGAAACACACAA
ATATGATGATCCAAAAGTAAAATTAGGAAAC

Alignment

ORF - retro_chof_1782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.04 %
• Parental protein coverage: 98.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WLNFLIFLCGSAIGFFL--CSQLFSILLEEQ-SDTQPNILHNDPHARHSDDNGQNHLEGQMNFNADTSQH
          WLNFLIFL.GSAIG.....CSQLFSILLEE..SDTQ.N..HNDPHARH.D.N.QNHLEGQMNF.AD.SQH
Retrocopy WLNFLIFLHGSAIGXXXXXCSQLFSILLEER<SDTQANTFHNDPHARHADGNRQNHLEGQMNFSADVSQH

Parental  KDEDTDIAEKLYQKVKILCWVMTGPQNLEKKAKHVKATWAQRCNKVLFMSSEENKDFPTVGLKTKEGRDQ
          KD.DTD.AEKLYQK.KILCWVMTGPQN.EKKAKHVKATW.Q.CN.VLFMSSEENKDFPTVGLKTK.GR.Q
Retrocopy KDDDTDLAEKLYQKIKILCWVMTGPQNSEKKAKHVKATWTQCCNEVLFMSSEENKDFPTVGLKTK-GREQ

Parental  LYWKTIKAFHYVYDHHLEDADWFMK-ADDDTYVILDNLRWLLSKYDPEKPIYFGRRFKPFVKQGYMSGGA
          LYWKTIKAF.YVYDH.LED.DW..K.ADDDT..I.DNLR.LLSKYDPEKPIYFGRRFKP.VKQ.YMSGGA
Retrocopy LYWKTIKAFQYVYDHYLEDGDWLRK<ADDDTHFIRDNLRCLLSKYDPEKPIYFGRRFKPYVKQAYMSGGA

Parental  GYVLSKEALKRFVDAFRTDKCTHSSSIEDLAL-GRCMEIMNVEAGDSRDTTGKETFHPFVPEHHLIKGYL
          G.VLSKEALKRFVDAF...KCTHSSSI.DLAL.GRCMEI..VEAGDSRDTTGKETFHP.VPEHHLIKGYL
Retrocopy GCVLSKEALKRFVDAFKAKKCTHSSSIKDLAL<GRCMEITDVEAGDSRDTTGKETFHPCVPEHHLIKGYL

Parental  PKTFWYWNYNYYPPVEGPGCCSDLAISFHYVDPLTMYELEYLVYHLRPYGYLYRYQPALSENRLREITE-
          .KTFWYW.YNY..PVEGPGC.SDLAISFHY.DPL..YELEYL.YHL.PYGYL.RYQPAL.EN.L..I.E.
Retrocopy SKTFWYWDYNYHSPVEGPGCYSDLAISFHYIDPLPTYELEYLIYHLHPYGYLHRYQPALPENILKKISET

Parental  -KNDDPKVKLGN
          .K.DDPKVKLGN
Retrocopy HKYDDPKVKLGN

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_1782 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000225	2 retrocopies	retro_chof_1782 , retro_chof_2581,
Dasypus novemcinctus	ENSDNOG00000017353	2 retrocopies	retro_dnov_1801, retro_dnov_1905,
Homo sapiens	ENSG00000106392	2 retrocopies	retro_hsap_3177, retro_hsap_4065,
Loxodonta africana	ENSLAFG00000000063	1 retrocopy	retro_lafr_1166,
Myotis lucifugus	ENSMLUG00000014789	1 retrocopy	retro_mluc_1310,
Macaca mulatta	ENSMMUG00000016338	1 retrocopy	retro_mmul_2009,
Oryctolagus cuniculus	ENSOCUG00000026002	1 retrocopy	retro_ocun_216,
Otolemur garnettii	ENSOGAG00000012847	1 retrocopy	retro_ogar_855,
Petromyzon marinus	ENSPMAG00000001562	1 retrocopy	retro_pmar_2,
Pan troglodytes	ENSPTRG00000018925	2 retrocopies	retro_ptro_2266, retro_ptro_2755,