RetrogeneDB ID: retro_lafr_460

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_17:14664044..14665094(-)
• Located in intron of: ENSLAFG00000011392

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDG
• Ensembl ID: ENSLAFG00000003813
• Aliases: None
• Description: None

Sequence

>retro_lafr_460
AGTTATTCCCTTCATCAGGCTCAAGCTTTTTATACATTCCTGTTTCAACAAATCATGACCAAAGCTCCTAATATGGGAAC
CATGAACGAACAGCAAATGCCAGCAGAGGTTCCAGTCCTAGCCCCTGCTGAGGAAGGAGCTTGTACAAGAGGCTCTAAAA
GGAAGTAAAAGAAAACCTAGAACAACAGAACCAAAAAGCCAGTGGAACTCAAAAAACCTGCTGCACCAAAAGAAATCTGG
CAAGTCCACAAAATCAAAAGAAAAACAATAAAACATGACAGACACATTTAAAGTGAAAAGAAAAGTAGACCATTTTAATG
GTATTTCAGAAGCTGAACTTTTAACCAAGACTCCCCCTGATATTTTGACCTTTAATCTGGATATTGTGATTACTGACATA
AACCCAGGACTAAGGGCTGCTTACAAAGAACATCACTACCCTGGCCTTGGGAACCGTTTTTGGAAGTGTCTGTTTACATT
GGGGCTGAATGAGGTCCAGCTGAATCATATGATCACACTTTACCAGGGAAGATATGGTGTTGGATTTACCAATATGATGT
AAAGGACTGCGCCAGGCAGCAAGGATCTTTCCAGTAAAGAAATTCATGAAGGAGGACATATTCTAGTGCAGAAATTACAG
AAATAACAGCCACGAATAGTGGTGTTTAATGGAAAATATATTTATGAAATTTTTAGCAAATAAGTTTTTGGAGTAAAGGT
TAAGGACTTAGAATTTGGACTTCAACCCCGTAAGATCTCAGACACTGAAACTCTCTGCTGTTATGCCACCATCCAGTGCA
GGGTGTGCTCAGGTTCCTCCAGCCCAAGACAAAGATCATTACTGCGTTAAACTGAAGGACTTAAGAGATCAGTTGAAAGG
CATTGAAGGAAACAGAGATATTCAGGAGGTGCAATATATGTTTGACTTAACACCTTGCCCAAGAGGATGCAAAGAAGATA
GCTGTTAAGGAAGAAAAATATGATCTGGGTTATGAAGCAGCATATGATGGTGCTTATGGTGAAAATCCATGCAACAGTGA
AACAGCTTCT

Alignment

ORF - retro_lafr_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.31 %
• Parental protein coverage: 85.16 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SCSLRQAQAFYTFRFQQMLAEAPNMETVNEQQVPVEVLVTAPAQEPLPEAPKGRKRKPRTT---EPKKPV
          S.SL.QAQAFYTF.FQQ....APNM.T.NEQQ.P.EV.V.APA.E.......G.KRK...T.....KKPV
Retrocopy SYSLHQAQAFYTFLFQQIMTKAPNMGTMNEQQMPAEVPVLAPAEE--GACTRGSKRK*KKT*NNRTKKPV

Parental  EPEKPAVP-KKSGKSTKSKEKQEKITDTFKVKRKVDRFNGVSEAELLTKTLPDILTFNLDIVIIGINPGL
          E..KPA.P.KKSGKSTKSKEKQ...TDTFKVKRKVD.FNG.SEAELLTKT.PDILTFNLDIVI..INPGL
Retrocopy ELKKPAAP>KKSGKSTKSKEKQ*NMTDTFKVKRKVDHFNGISEAELLTKTPPDILTFNLDIVITDINPGL

Parental  MAAYKGHHYPGPGNHFWKCLFMSGLSEVQLSHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGR
          .AAYK.HHYPG.GN.FWKCLF..GL.EVQL.HM......G.YG.GFTNM..RT.PGSKDLSSKE..EGG.
Retrocopy RAAYKEHHYPGLGNRFWKCLFTLGLNEVQLNHMIT-LYQGRYGVGFTNMM*RTAPGSKDLSSKEIHEGGH

Parental  ILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLC-YVMPSSSARCAQFPRA
          ILVQKLQK.QPRI.VFNGK.IYEIFSK.VFGVKVK.LEFGLQP.KI.DTETLC....PS.SA.CAQ.P.A
Retrocopy ILVQKLQK*QPRIVVFNGKYIYEIFSK*VFGVKVKDLEFGLQPRKISDTETLC>VMPPS-SAGCAQVPPA

Parental  QDKVHYYIKLKDLRDQLKGIERNTDVQEVRYTFDL-QLAQEDAKKMAVKEEKYDPGYEAAYGGAYVENPC
          QDK.HY..KLKDLRDQLKGIE.N.D.QEV.Y.FDL..LAQEDAKK.AVKEEKYD.GYEAAY.GAY.ENPC
Retrocopy QDKDHYCVKLKDLRDQLKGIEGNRDIQEVQYMFDL>HLAQEDAKKIAVKEEKYDLGYEAAYDGAYGENPC

Parental  NSEPCS
          NSE..S
Retrocopy NSETAS

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_460 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013722	1 retrocopy	retro_dnov_1749,
Echinops telfairi	ENSETEG00000019930	1 retrocopy	retro_etel_2184,
Homo sapiens	ENSG00000139372	1 retrocopy	retro_hsap_980,
Loxodonta africana	ENSLAFG00000003813	1 retrocopy	retro_lafr_460 ,
Mus musculus	ENSMUSG00000034674	4 retrocopies	retro_mmus_1125, retro_mmus_1363, retro_mmus_3040, retro_mmus_637,
Oryctolagus cuniculus	ENSOCUG00000016313	1 retrocopy	retro_ocun_1289,
Rattus norvegicus	ENSRNOG00000027124	1 retrocopy	retro_rnor_2286,