RetrogeneDB ID: retro_lafr_948

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:96114587..96115360(-)
• Located in intron of: ENSLAFG00000000453

Retrocopy information

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

Parental gene information

• Parental gene symbol: APEX1
• Ensembl ID: ENSLAFG00000021872
• Aliases: None
• Description: None

Sequence

>retro_lafr_948
GGTCAACCTGCCACACTTCACATCTGCTCCTGGAATGCGGGTGGGCCTCGAGCCTGGAATAAGGAGAAAGGTTTAGGTTG
GATAAAGAAAGAAGCCCCAGATATTCTGTGCCTCCAAGAAACCAAATGTTCAGAGGAAAAACTACCACCAGCTGAACCTC
AAGACCTGCCTGGACTATCTCCTCAGTTCTGGTCGGCTCCTTCAGACAGGGAAGGGTACAGTGGTGTGGGTCTACTGTCC
TGCTGGTGGCCTCACAAAGTCTTTTACGGCATTGGCAGGGAGGAACATGACCAGGAAGGCCAGTGATGGTGGCTGAATTT
AATGAATTTGTTCTGGTAACAGCCTATGTATCTAATGCAGGCCGGAGTATGGGACGAATAGAATACCAGCAGCGCTGGAA
TGAAGCCTTTGGCAAATTCCTGAGGGACCTGGCTTCACACAACCCTCTTGTGCTATGCGAGGACCTCAACGTGGCTCATG
AAAAGATAGGCCTTTGCAACCCAAAGGGAAACAAGAAAAATTCTGGCTTTACTCAACAAGAGTGCCAAGGCTTTGGGAAA
TTATGGCAAGCTGTGCCACTGACTAACAGCTTCCGGCACCTCTGCCCCAATACAGCCTATGCCTGTATCTTTGTATCTAC
CTGTTGAATGCTTGATCCAACAATGTTGACTGGTGCCTTGATTATTTTTTTGTTGTGTTACTCTCTGTTACTTGCATTGT
GTGATAGCAAGATCCGTCCTAAGACCTTAGACAGTGATCACTGTCCCAGCACC

Alignment

ORF - retro_lafr_948 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.26 %
• Parental protein coverage: 80.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GKSATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSEKKLP-AELQDLPGLSHQYWLAPSDK
          G..ATL.ICSWN..G.RAW.K.KGL.W.K.EAPDILCLQETKCSE.KLP.AE.QDLPGLS.Q.W.APSD.
Retrocopy GQPATLHICSWNAGGPRAWNKEKGLGWIKKEAPDILCLQETKCSEEKLPPAEPQDLPGLSPQFWSAPSDR

Parental  EGYSGVGLLSRQCPLKVSYGIGEEEHDQEGR-VIVAEFDAFVLVTVYVPNAGRGLVRLDYRQRWDEAFRK
          EGYSGVGLLS...P.KV.YGIG.EEHDQEG..V.VAEF..FVLVT.YV.NAGR...R..Y.QRW.EAF.K
Retrocopy EGYSGVGLLSCWWPHKVFYGIGREEHDQEGQ<VMVAEFNEFVLVTAYVSNAGRSMGRIEYQQRWNEAFGK

Parental  FLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPDTAYAY
          FL..LAS..PLVLC.DLNVAHE.I.L.NPKGNKKN.GFT.QE.QGFG.L.QAVPL..SFRHL.P.TAYA.
Retrocopy FLRDLASHNPLVLCEDLNVAHEKIGLCNPKGNKKNSGFTQQECQGFGKLWQAVPLTNSFRHLCPNTAYAC

Parental  TFWT-YMMNARSKNVGWRLDY-FLLSHSLLPALCDSKIRSKALGSDHCPIT
          .F...Y..NA.S.NV.W.LDY.FLL..SLL.ALCDSKIR.K.L.SDHCP.T
Retrocopy IFVS<YLLNA*SNNVDWCLDY>FLLCYSLLLALCDSKIRPKTLDSDHCPST

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_948 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002745	1 retrocopy	retro_btau_1729,
Echinops telfairi	ENSETEG00000004855	1 retrocopy	retro_etel_1392,
Loxodonta africana	ENSLAFG00000021872	1 retrocopy	retro_lafr_948 ,
Mus musculus	ENSMUSG00000035960	2 retrocopies	retro_mmus_2027, retro_mmus_433,
Otolemur garnettii	ENSOGAG00000013335	3 retrocopies	retro_ogar_1284, retro_ogar_2145, retro_ogar_3243,
Rattus norvegicus	ENSRNOG00000009663	1 retrocopy	retro_rnor_2971,
Ictidomys tridecemlineatus	ENSSTOG00000010096	1 retrocopy	retro_itri_1560,
Tupaia belangeri	ENSTBEG00000006405	1 retrocopy	retro_tbel_3409,