RetrogeneDB ID: retro_lafr_1109

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_7:26427832..26428701(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSLAFG00000007533
• Aliases: None
• Description: None

Sequence

>retro_lafr_1109
GTGAAAGCACTGAAAAGGAAGATTAAATCTGAAAACGGGAAAGATGCCTTTCTGGTGCAGGCCAAAAATTAATTTACACA
GGCAAAATCCTCACTGATACTATTCTCAAATATAAAATTGGTGAGAAAAATTTTTGTGGTGGCTATGGTGACAAAACCTA
GAGCAATGACAACATCAGCACCAGCGACAACTCAGCAATCACTTTCTGCCACCATTACTGCAGTTAGCTCCCCTGCTGCA
GCAGCTGTGGTTCAGGCCCAGCCCTGGCCCTGCTTTGGGCCCCACTTCCACACCTACATCCATCACTCCAACGTCAACAA
CAGCGTCTTCTGAACTTGAACCTGCGAGCACTACTAAACAAGAGCAGCCTGCTGAAACGCCAGCAGAAACATCAGTGGCT
ACCAGTCCAACATCAGTGGAGAGTAATCAGGAGATTCTTCTCGGTCAAACCTTTTTGAACACGTGGCAAGGGCAGTTGAG
ATAGGTCAGTCCTATGAGAATATGGAAACTGAGATCATCTCCACGGGCTTTGAGCAGAAGCAAGTAATTACAGCTCTGAG
AGCCAATTTCAACAACCCTGACTGAACAGTGGAGTATCTCTTAATAGGAATCCCTGACAGTCAGGATGTGGTTGACTCCC
TTCAAGCAGCTAGTACTGGGGGACCTCAGTCTTCAGCAGTGTCTGCACTACAGCAAGTGTGACAGCAATGACTACAAGTT
CTGGAGGAAATCTCTTTGAATTTTTATGGAATCAACCTCAGTTCTGACAGATGAGATAAATTATTCTATAGAATCCTTCT
CTGCTTCCAGTACTGCTGCAATGGATGGGTTGAAAGAATCCTCAATTACTGCAACAAATGAGAAAACAT

Alignment

ORF - retro_lafr_1109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.99 %
• Parental protein coverage: 77. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VKALKEKIESEKGKDAFPV-AGQKLIYAGKILNDDTALKEYKIDEKNF-VVVMVTKPKAVTTPAPATPQQ
          VKALK.KI.SE.GKDAF.V.AGQKLIY.GKIL.D.T.LK.YKI.EKNF.VV.MVTKP.A.TT.APAT.QQ
Retrocopy VKALKRKIKSENGKDAFLV<AGQKLIYTGKILTD-TILK-YKIGEKNF>VVAMVTKPRAMTTSAPATTQQ

Parental  SNPATTAAVSSSTAAAVAQA-PAPAPALAPTSTPTSITPASTTASSEPAPASATQQEKPTEKPTETPVAA
          S..AT..AVSS..AAA.....P.P.PAL.PTSTPTSITP.STTASSE..PAS.T.QE.P.E.P.ET.VA.
Retrocopy SLSATITAVSSP-AAAAVVQ>PSPGPALGPTSTPTSITPTSTTASSELEPASTTKQEQPAETPAETSVAT

Parental  SPTSTDST-SGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLMG
          SPTS..S..SGDSSRSNLFE....A...GQSYENM.TEI.S.G.E..QVI.ALRA.FNNPD..VEYLL.G
Retrocopy SPTSVESN<SGDSSRSNLFEHVARAVEIGQSYENMETEIISTGFEQKQVITALRANFNNPD*TVEYLLIG

Parental  IPGDRESQAVVDPPQAASTGTPQSSAVAA-AAATTTATTTTTSSGGHPLEFLRNQPQFQQMRQIIQQNPS
          IP....SQ.VVD..QAASTG.PQSSAV.A...A..TA...TTSSGG...EFL.NQPQF.QMR.II..NPS
Retrocopy IP---DSQDVVDSLQAASTGGPQSSAVSA<TTASVTA--MTTSSGGNLFEFLWNQPQF*QMR*IIL*NPS

Parental  LLPALLQQIGRENPQLLQQISQH
          LLP.LLQ..G..NPQLLQQ...H
Retrocopy LLPVLLQWMG*KNPQLLQQMRKH

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_1109 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Dasypus novemcinctus	ENSDNOG00000001174	2 retrocopies	retro_dnov_1982, retro_dnov_989,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Loxodonta africana	ENSLAFG00000007533	1 retrocopy	retro_lafr_1109 ,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,