RetrogeneDB ID: retro_lafr_1166

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:7474164..7475253(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000029994
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C1GALT1
• Ensembl ID: ENSLAFG00000000063
• Aliases: None
• Description: None

Sequence

>retro_lafr_1166
ATGACCTTCAAATCTTGGCTGCATTTTTTACCCTTCCTCTGTGGATCTGCAATTGGATTTTTGTTATGTTCTCAACTCTT
CAGTATTTTGTTGGAAGAACAGAGTGACACCCAGCTTAAAATTCTTAATAATCATCCTCTTGCCAGGCATCCAGATGGTG
CTGGACAGAATTTTCTAGAAAGACAGATGATGTTCCACGCAGATCCATACCAGCGTACAGGTGAGAACGCTGATGTCGCT
GAAACACTCTATCGAGAAGTTAAAATCCTTTGCTGGGTTATGACGGGGCCTCAAAATCTGGAGCAAAGGGCCAAACACGT
CAAAGCCACGTGGGCCCAGCGTTGTAATAAGGTCTTGTTTATGAGTTCAGAGGAAAATAAAGACTTCCCTACCGTGGGAC
TAAACACCCAAGAAGGGAGACACCAACTGTCCTGGAAAACAATCCGAGCCTTTCAGTATGTTCATGACCATTGTTTAGAA
GAGGCAGACTGGTTTATGAAAGCAGATGACGACACATATGTCATACTAGACAATTTGAGATGGCTTCTCGCAAATTATGA
TCCCCAAGAACCTATTTACTTTGGGAGAAGATTCCGGCCGTTTGTAAAGCAGGGATACATGAGCGGTGGGGCAGGGTATG
TGCTCAGCAAGGAAGCCTTGAAGAGGTTTGTGCACGCCTCTAAAACGAACACGTGTACACCTGCCACGCCCGTTGAAGAC
TTAGAACTGGGGATATGCATGGAAATCGTAAAGGTACACGCGGAAGATTCCAGAGATCCCACTGGCAAAGAAACTTTTCA
TCCTTTTTTGCCAGAATACCATTTAAGCAAAGGCGTTCTGCCCAGAACCTTTTGGTACTGGAGGTATAACTATTACCTGC
CTGTAGAGGGTCCGGGTTGCTGTTCTGATTTTGCCATTTCTTTTCATGGTGTGCCCCTGACATTCATGTATGAGTTAGAA
TACCTGGTGTATCACCTTCGTCCCTATGGTTACTTGTACAGATATCAACCTGCCTTACCTGAGAGTCCACAAAAAGGAAA
CAAGCAAAGCAAACAAAAATGAAGATCCAAAATTAAACTTAGAGAGCCC

Alignment

ORF - retro_lafr_1166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASKSWLNFLTFLCGSAIGFFLCSQLFSILLGEQGDIQPNILHNDPHARHSDDNGHNHLEGQMNFNADAS
          M..KSWL.FL.FLCGSAIGF.LCSQLFSILL.EQ.D.Q..IL.N.P.ARH.D..G.N.LE.QM.F.AD..
Retrocopy MTFKSWLHFLPFLCGSAIGFLLCSQLFSILLEEQSDTQLKILNNHPLARHPDGAGQNFLERQMMFHADPY

Parental  QHTDENTDISEKLYQKVKILCWVMTGPQNLEKKAKHVKATWAQRCNKVLFMSSEENKDFPTVGLKTKEGR
          Q.T.EN.D..E.LY..VKILCWVMTGPQNLE..AKHVKATWAQRCNKVLFMSSEENKDFPTVGL.T.EGR
Retrocopy QRTGENADVAETLYREVKILCWVMTGPQNLEQRAKHVKATWAQRCNKVLFMSSEENKDFPTVGLNTQEGR

Parental  DQLYWKTIKAFQHVHDHYLEDADWFMKADDDTYVVLDNLRWLLSKYDPEKPIYFGRRFKPYVKQGYMSGG
          .QL.WKTI.AFQ.VHDH.LE.ADWFMKADDDTYV.LDNLRWLL..YDP..PIYFGRRF.P.VKQGYMSGG
Retrocopy HQLSWKTIRAFQYVHDHCLEEADWFMKADDDTYVILDNLRWLLANYDPQEPIYFGRRFRPFVKQGYMSGG

Parental  AGYVLSKEALKRFVDAFKTDKCTHSSSIEDLALGRCMEIINVEAGDSRDTTGKETFHPFVPEHHLIKGYL
          AGYVLSKEALKRFV.A.KT..CT.....EDL.LG.CMEI..V.A.DSRD.TGKETFHPF.PE.HL.KG.L
Retrocopy AGYVLSKEALKRFVHASKTNTCTPATPVEDLELGICMEIVKVHAEDSRDPTGKETFHPFLPEYHLSKGVL

Parental  PKTFWYWNYNYYSPVEGPGCCSDLAVSFHYVDPTTMYELEYLIYHLRPYGYLYRYQPALPEEISEAYKNE
          P.TFWYW.YNYY.PVEGPGCCSD.A.SFH.V..T.MYELEYL.YHLRPYGYLYRYQPALPE......K..
Retrocopy PRTFWYWRYNYYLPVEGPGCCSDFAISFHGVPLTFMYELEYLVYHLRPYGYLYRYQPALPESPQKGNKQS

Parental  D----SKVKLGNP
          .....SK.KL..P
Retrocopy KQK*RSKIKLREP

Legend:

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

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_1166 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana 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,