RetrogeneDB ID: retro_lafr_147

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:99650394..99651552(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMP12
• Ensembl ID: ENSLAFG00000010062
• Aliases: None
• Description: None

Sequence

>retro_lafr_147
TTGGTGATGATGCACATCCCTCAGTGTGGCATGACTGACATTCATCATTAGACTACAATGCCAGGGAGGCCAAGATGGAA
AAAACATCATATCAAATACAGAATCCAGAATTACACTCCTGACTTAGTGCATGAGGATGTTAACTACGTCATCCAGAAAG
GTTTTCAAGTAAGGAGTGATGTCAGCCCTTTGAAATTCAAACAGATGAATGCAGGCAAATACTTACATTCTGGTATTTTT
TTCACATGGAGCTTACAGAGATTTCAATCTTTTTAATAGTGGAGGTGGAGTCATAGCCCAACCTTTTGCACCTGAACTGG
TATTGGAGGAAATGCACATTTTGATGTGGATGAAATCTGGACTAAAAGTTCCAAAGGCACAAACTTGTTTCTTGTTGCTG
TTCAGGAGGTTAGTCTTTCCTTGGGTCTCAAACATTGCAATGATCCAAAGGCCATAATGTTCCCCACCTACAGTTACGTC
GACACCAACGCATTTTGCCTCTCTACTGATGACATATGTGGTATCCAGTCCCTTTATGGAGGACCAGAAAAGCACCAACG
CGTGCCACCTTCTGACAGTACAGAATCAATTAGCTGTGACCCCAACTTGAGTTTTGATGCTGTCACTACACTCAGAGATA
GAAACTTTTCCTTTAAAGACATGCTCTTCTGCTGGAAGTTTCCTGAGTTATCAAGAAGCAGTCTTTGTTTAATTTCTTCC
TTATGGCCAACCTTGCCATCTGTCATTCAAGTCACTTACGAAATTAGAGCCAGATATCAAGTTTTTTCTTTTTAAAGATG
ACAAGTACTGGCTAATTAGCAATTTAAGAGCATAGCCAAATTATCCCAAGAGCATACATTCTTTGGGCTTCCTTGACTCT
GTAAAAAAACTGATGTAACTGTTTTTAACTCACTTATCTACAAAACTTACTCTTTGTAGGTAATCAGTATTGGAGGTATG
ATGAGAGGAGACAATTTATGGAGCACGGTTATCTCAAATTGATAACCAAGAAATTCCCAGGAATTGGGCCTAAAATTGAT
GCATCCTTCCATTCTAAAAGAAACTATTGTTTTTTTCCAAGGATCTACCTAACTCGAATATGACATCTAATCCAATCACA
TCACCAAAAGACTGAGAAGCAATAGTGGTTTTGGTTGT

Alignment

ORF - retro_lafr_147 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.9 %
• Parental protein coverage: 81.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LEMMHTPRCGMPDVRHYSTMPGRPVWKKGHITYRIQNYTPDMAREDVNYAIQKAFQVWSDVTPLTFRQIY
          L.MMH.P.CGM.D..H..TMPGRP.WKK.HI.YRIQNYTPD...EDVNY.IQK.FQV.SDV.PL.F.Q..
Retrocopy LVMMHIPQCGMTDIHH*TTMPGRPRWKKHHIKYRIQNYTPDLVHEDVNYVIQKGFQVRSDVSPLKFKQMN

Parental  AGE-ADIMIFFAQGAHGDFYPFDGRGGVIAHAFAPG-TGIGGDTHFDESEIWTKGFKGINLFLVAVHELG
          AG....I..FF..GA..DF..F...GGVIA..FAP..TGIGG..HFD..EIWTK..KG.NLFLVAV.E..
Retrocopy AGK>TYILVFFSHGAYRDFNLFNSGGGVIAQPFAPE<TGIGGNAHFDVDEIWTKSSKGTNLFLVAVQEVS

Parental  HSLGLNHSNDRKAIMFPTYSYVDTKTFRLSTDDIRGIQSLYGGPEKYQPMPPPDSTESTICDPNLSFDAA
          .SLGL.H.ND.KAIMFPTYSYVDT..F.LSTDDI.GIQSLYGGPEK.Q..PP.DSTES..CDPNLSFDA.
Retrocopy LSLGLKHCNDPKAIMFPTYSYVDTNAFCLSTDDICGIQSLYGGPEKHQRVPPSDSTESISCDPNLSFDAV

Parental  TIIGNRIFFFKDRFFWWKFPESSRISVNLISSLWPTLPSVIQAAYEIKARNQV-FLFKDDKYWLISHLRP
          T....R.F.FKD..F.WKFPE.SR.S..LISSLWPTLPSVIQ..YEI.AR.QV.FLFKDDKYWLIS.LR.
Retrocopy TTLRDRNFSFKDMLFCWKFPELSRSSLCLISSLWPTLPSVIQVTYEIRARYQV>FLFKDDKYWLISNLRA

Parental  QPNYPKSIRSLGFPGSVKKI-DAAVFNPLIYKTY-FFVDNQYWRYDERTQSMDHGYPKLITKNFPGIGPK
          .PNYPKSI.SLGF..SVKK..D..VFN.LIYKTY..FV.NQYWRYDER.Q.M.HGY.KLITK.FPGIGPK
Retrocopy *PNYPKSIHSLGFLDSVKKL<DVTVFNSLIYKTY<LFVGNQYWRYDERRQFMEHGYLKLITKKFPGIGPK

Parental  IDAVFYSKKHY-YFFQGSNQLEYDVQSNRVTRRLKSNDGFGC
          IDA.F.SK..Y..FFQGS..LEYD..SN..T.RL.SN.GFGC
Retrocopy IDASFHSKRNY>VFFQGST*LEYDI*SNHITKRLRSNSGFGC

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_147 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008413	6 retrocopies	retro_chof_1424, retro_chof_1611, retro_chof_2207, retro_chof_325, retro_chof_595, retro_chof_645,
Equus caballus	ENSECAG00000019445	1 retrocopy	retro_ecab_153,
Loxodonta africana	ENSLAFG00000010062	1 retrocopy	retro_lafr_147 ,
Macaca mulatta	ENSMMUG00000004250	1 retrocopy	retro_mmul_2325,
Otolemur garnettii	ENSOGAG00000010221	1 retrocopy	retro_ogar_965,