RetrogeneDB ID: retro_chof_2581

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_87587:2031..3109(-)
• 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_2581
ATGGCCTCTAAATCTTGGCTGAATTTTTTAATCTTCTTCTGTGGATCAGCAATCGGATTTTTTTTAATGTTCTCAGCTGT
TTAGTATTTTATTGGAAGAACAAAGTGATACCCAAGCTAATATTCTTCCTAACGATCCTCATGCTAAACATTCGGATGAG
AAGCAACAGACTCATCTAGAAGGACAGATCCACCTCAATACGGCACCAGCCAAGGAAAGATGAGGACACAGACATCGCTG
AAAAACTCTATCGGAAGCTTAAAATTCTTTGCTGGCTTATGACAGGACCTCAAACTTTAGAGAAAAAGGCCAAACACATC
AAAGCCACATGGACTCAATGTTGTAATAAAGTTTTGTTTATGAGTTCAGAAGAAAATAAAGACTTCCCAACCGTGGAATC
AAAAAACAAAGAAGGCAGAGACCAACTATATTGGAAAACAAAGCTTTACTACATATTTATGACCACTATTCAGAAGATGC
TGATTGGTTCATGAAAGCAGATGATGATATATAGGTCCTAGTAGACAATTTGAGATGGCTTCTTTCCAAATATGACCCTG
AAAAACCCATTCACTTTGGGAGAAGATTTAAGCCCTATGTAAAGCAGGCCTACATGAGTGGAGGAGCAGAAAATGTATTG
AGCAAGGAAGCCAGGAAGAGATCTGTTGATGCATTTAAAATGGACAGATGTACACATAGTCCTCCATCGAAGACTTAGCA
CTGGGACATGCATGGAAATTATAGATGTAGAAGCTGGAGATTCCAGAGATACCACTAGAAAAGAAACCTTTCATCCCTGT
GTACCAGAACACCACTTAATCAAAGGTTATCCATCCAAAACCTTTCGGTACTGGGATTATAACTATTATCCTCCTGCAGA
GGGTCCTGGATGCTGTTCTGATCTTGCAATTCCTTCTCGTTTGTTGACCCTCTCATTATGTATGAGTTAGAATACCTCAT
TTACCATCTTCACCCATATAGTTATTTACACAGATATCAACCTGCTTTACCCGAGAATATATTAAAGGAAATAAGTGAAA
CATACAAAAATGATGATTCAAAAGTAAAATTAGGAAAC

Alignment

ORF - retro_chof_2581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.42 %
• Parental protein coverage: 99.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MASKSWLNFLIFLCGSAIGFFL-CSQLFSILLEEQSDTQPNILHNDPHARHSDDNGQNHLEGQMNFNA-D
          MASKSWLNFLIF.CGSAIG....CSQLFSILLEEQSDTQ.NIL.NDPHA.HSD...Q.HLEGQ...N...
Retrocopy MASKSWLNFLIFFCGSAIGXXX>CSQLFSILLEEQSDTQANILPNDPHAKHSDEKQQTHLEGQIHLNT<G

Parental  TSQ-HKDEDTDIAEKLYQKVKILCWVMTGPQNLEKKAKHVKATWAQRCNKVLFMSSEENKDFPTV-GLKT
          TSQ..KDEDTDIAEKLY.K.KILCW.MTGPQ.LEKKAKH.KATW.Q.CNKVLFMSSEENKDFPTV.G.K.
Retrocopy TSQ<RKDEDTDIAEKLYRKLKILCWLMTGPQTLEKKAKHIKATWTQCCNKVLFMSSEENKDFPTV<GIK-

Parental  KEGRDQLYWKTIKAFHYVYDHHLEDADWFMKADDDTYVILDNLRWLLSKYDPEKPIYFGRRFKPFVKQGY
          K..R........KA....YDH..EDADWFMKADDD..V..DNLRWLLSKYDPEKPI.FGRRFKP.VKQ.Y
Retrocopy KQRRQRPTILENKALLHIYDHYSEDADWFMKADDDI*VLVDNLRWLLSKYDPEKPIHFGRRFKPYVKQAY

Parental  MSGGAGYVLSKEALKRFVDAFRTDKCTHS-SSIEDLALGR-CMEIMNVEAGDSRDTTGKETFHPFVPEHH
          MSGGA..VLSKEA.KR.VDAF..D.CTHS.SSIEDLALG..CMEI..VEAGDSRDTT.KETFHP.VPEHH
Retrocopy MSGGAENVLSKEARKRSVDAFKMDRCTHS<SSIEDLALGH<CMEIIDVEAGDSRDTTRKETFHPCVPEHH

Parental  LIKGYLPKTFWYWNYNYYPPVEGPGCCSDLAI-SFHYVDPLTMYELEYLVYHLRPYGYLYRYQPALSENR
          LIKGY..KTF.YW.YNYYPP.EGPGCCSDLAI.SF..VDPL.MYELEYL.YHL.PY.YL.RYQPAL.EN.
Retrocopy LIKGYPSKTFRYWDYNYYPPAEGPGCCSDLAI<SFSFVDPLIMYELEYLIYHLHPYSYLHRYQPALPENI

Parental  LREITE--KNDDPKVKLGN
          L.EI.E..KNDD.KVKLGN
Retrocopy LKEISETYKNDDSKVKLGN

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_2581 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,