RetrogeneDB ID: retro_lafr_1104

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_7:88344760..88345459(+)
• Located in intron of: ENSLAFG00000017730

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIPIN
• Ensembl ID: ENSLAFG00000026016
• Aliases: None
• Description: None

Sequence

>retro_lafr_1104
CAAAGAGAAGTTAAAAGGAATATACCAAGCTGGATGCTCAGATATTAATTTCAGAGGGAGGGCTTCCAGTCTTAAGGCAT
GTGTTTGATAAGGCAAAATTCAAAGATAAAGGTCACGAGGCTGAAGACTTGAAGAAGCTAATCAGACACATGGAGCACTA
GGCACATAGGCTATTCCTAACTGTAATTTCAGGATTTTTATTCACAGAGTTGAATACCTGGGAAATAAAAGGTAAGTTCA
GATCTGTTTAAAGTAAATTCGACTTGATCTCCCTGTTTTACATAAAGATTTTACCAACAATAATGATGAAGTAGGGGAAA
ATAATGGCGATGATGTAACTGCTACTGAATTAGATCCTTTTTTGACAAGCTCATCTGAAAGTGAGAGGTTTGTTTCTGAG
TCAAGTAGAAGCCTAAAAGAAGAGCTACAACAACAACAACAACAAACTAGAGAAATAAACAACTGGCCTAGAAAAGAAGG
CAAGCATAGCTGCTGAGTAACAGTCAGTGCCTAGGAAATGACTTGCTAACGGACACACCCAGGGCACAGACAGTTGGAGA
GGTCAATACAAGTGAAGACCAATAAGAGGAGGAGTCAAATGGATTAGGTGAAGACATTCCAGAAAATTCACACAATGATG
CTGCCAATACTGTAAATGTAGAGGAGGAATTAAAATTAGAGAAAATGCAACTGGACCAA

Alignment

ORF - retro_lafr_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.95 %
• Parental protein coverage: 81.49 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KRTIKRNIP-KLDAQRLISERGLPALRHVFDKAKFKGKGHEAEDLKKLIRHMEHWAHRLF-PKLQFEDFI
          .R..KRNIP.KLDAQ.LISE.GLP.LRHVFDKAKFK.KGHEAEDLKKLIRHMEH.AHRLF.P...F..FI
Retrocopy QREVKRNIP<KLDAQILISEGGLPVLRHVFDKAKFKDKGHEAEDLKKLIRHMEH*AHRLF<PNCNFRIFI

Parental  DRVEQLGNKKEVQQTCLKRIRLDLPILHEDFVNNNDEVGENNEDDVTAAELDPFVTNSPERGKFASESSR
          .RVE.LGNK..VQ..CLK.IRLDLP.LH.DF.NNNDEVGENN.DDVTA.ELDPF.T.S.E...F.SESSR
Retrocopy HRVEYLGNKR*VQ-ICLK*IRLDLPVLHKDFTNNNDEVGENNGDDVTATELDPFLTSSSESERFVSESSR

Parental  SLTEE---QQQRIE-RNKQLALERRQAKLLTNSQSLGNDL--DSPRAQTAGEVNTSEDQKEEESNGLNVD
          SL.EE...QQQ....RNKQLA..RRQA.LL.NSQ.LGNDL..D.PRAQT.GEVNTSEDQ.EEESNGL..D
Retrocopy SLKEELQQQQQQTR<RNKQLA*KRRQA*LLSNSQCLGNDLLTDTPRAQTVGEVNTSEDQ*EEESNGLGED

Parental  ILENPH-DAENTVNVKEELKREETQLDQ
          I.EN.H.DA.NTVNV.EELK.E..QLDQ
Retrocopy IPENSHNDAANTVNVEEELKLEKMQLDQ

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_1104 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004860	1 retrocopy	retro_chof_223,
Dasypus novemcinctus	ENSDNOG00000003177	3 retrocopies	retro_dnov_1334, retro_dnov_1481, retro_dnov_410,
Homo sapiens	ENSG00000075131	1 retrocopy	retro_hsap_4837,
Gorilla gorilla	ENSGGOG00000000061	3 retrocopies	retro_ggor_1268, retro_ggor_2907, retro_ggor_3016,
Loxodonta africana	ENSLAFG00000026016	1 retrocopy	retro_lafr_1104 ,
Microcebus murinus	ENSMICG00000004386	2 retrocopies	retro_mmur_155, retro_mmur_255,
Macaca mulatta	ENSMMUG00000003695	1 retrocopy	retro_mmul_1582,
Nomascus leucogenys	ENSNLEG00000012909	1 retrocopy	retro_nleu_1336,
Pan troglodytes	ENSPTRG00000007192	2 retrocopies	retro_ptro_1145, retro_ptro_3220,
Rattus norvegicus	ENSRNOG00000043068	1 retrocopy	retro_rnor_364,