RetrogeneDB ID: retro_ogar_855

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873529.1:1695608..1696460(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1GALT1
• Ensembl ID: ENSOGAG00000012847
• Aliases: None
• Description: core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 [Source:HGNC Symbol;Acc:24337]

Sequence

>retro_ogar_855
TGTTCTAAGCTATTCAGTATTTTATTGGGAGAACAGAGCGATAACCAACCTAATACTCTTCATAATGACCTTCACGCTAG
GCATTCAGATGATCTTGGAGGGAATCACCTAGAAGGACAAATGAACTTCACCGTAGATGCTCCCCAACGTAAGGATGAGA
ACACAGACGCTGCTGAACATCTCTATCAGAAAGCTAAAACTCTGTGCTGAATTATGACAGGCTCTCAAAATCTAGAGAAA
AAGGCCAAGTACGTTAAAGCTACATGGGCGCAGTGTTGTAATAGAGTGTTGTTTTTGAGTTCAGAAGAAAATAAAGACTT
CCCTACTGTGGGACTAAAAACCAAAGAAGGCAGAGACCAACTATACTGGAAAACAATGGAAGCTTTTCACTATGTTCATG
ACCATTATTCAGAAGATGTTGGTTGGTTTATGAAAGCAGATGATGATACGTATGTCGTGGTGGACAACTTCAGATGGGTT
CTTTCAAAGTAGGACCCTAAAGAACCCATTTACTTTAGGAGAAGATCTGAGCACTATGTAAAGCAGGGTTACATGAGTGG
AGGAGCAGGATATGTACTAACAAAGAAGCCCTGAAGAGATTTGTCGATGCGTTTAAAACAGATAAATGTACACAGAGTTC
CTCCACTGAAGACTGAGCCCTGGGGAGATGCATGGACATTATGAATGTAGAAGTGGGAGATTCAAGAGGTACCACTGCAA
AAGAAACGTTTCATCCTTTTGTACCAGCACCATTTAATCAGAGGTTATCTACCCAGAACCTTTTGGTATTGGAATTGGAA
CTGTTATCCTCCTGCAGAGGGTCCTGGTTGCTGTTCTGATCTTGTGATGTCT

Alignment

ORF - retro_ogar_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.88 %
• Parental protein coverage: 78.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CSQLFSILLGQQSNNQPNILHNDPHARHSDDNGGNHLEGQMNFNVDASQHKDENTDIAEHLYQKVKILCW
          CS.LFSILLG.QS.NQPN.LHND.HARHSDD.GGNHLEGQMNF.VDA.Q.KDENTD.AEHLYQK.K.LC.
Retrocopy CSKLFSILLGEQSDNQPNTLHNDLHARHSDDLGGNHLEGQMNFTVDAPQRKDENTDAAEHLYQKAKTLC*

Parental  IMTGPQNLEKKAKHVKATWAQRCNKVLFMSSEENKDFPTVGLKTKEGRDQLYWKTIKAFHYVHDHYLEDA
          IMTG.QNLEKKAK.VKATWAQ.CN.VLF.SSEENKDFPTVGLKTKEGRDQLYWKT..AFHYVHDHY.ED.
Retrocopy IMTGSQNLEKKAKYVKATWAQCCNRVLFLSSEENKDFPTVGLKTKEGRDQLYWKTMEAFHYVHDHYSEDV

Parental  DWFMKADDDTYVIVDNLRWLLSKHDPKDPIYFGRRFKPYVKQGYMSGGAGYVL-SKEALKRFVDAFKTDK
          .WFMKADDDTYV.VDN.RW.LSK.DPK.PIYF.RR...YVKQGYMSGGAGYVL..KEALKRFVDAFKTDK
Retrocopy GWFMKADDDTYVVVDNFRWVLSK*DPKEPIYFRRRSEHYVKQGYMSGGAGYVL<NKEALKRFVDAFKTDK

Parental  CTHSSSIEDLAMGKCMEIMNVEAGDSRDTTGKETFHPFVP-EHHLIKGYLPRTFWYWNYNYYPPVEGPGC
          CT.SSS.ED.A.G.CM.IMNVE.GDSR.TT.KETFHPFVP..H.LI.GYLPRTFWYWN.N.YPP.EGPGC
Retrocopy CTQSSSTED*ALGRCMDIMNVEVGDSRGTTAKETFHPFVP>HH-LIRGYLPRTFWYWNWNCYPPAEGPGC

Parental  CSDLAIS
          CSDL..S
Retrocopy CSDLVMS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_855 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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,