RetrogeneDB ID: retro_lafr_1029

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:41924125..41925431(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028623
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KIAA0020
• Ensembl ID: ENSLAFG00000017341
• Aliases: None
• Description: None

Sequence

>retro_lafr_1029
CAAAGAAAAAAGTTGATGATCGATTTGCAGAAGTTGATTCAAGGGACAATTGAAACTATGGACTCCAAGTGTATGATCCA
GTGTTACATTCAATATAGAAATGAAGAGCAGAGAGAAGAGGCTTTCAAAGAATTGTAAAATAATTTGGTTGAAATTGAGT
AAAGGCAAATATTCCAGAAAGATTGTTAAGAAATTTTTTATGTATAGGAGCAAACCACAGATTGCAGATATCATCCGAAG
TGTCAAAGGTCATGTAAGGAAGATGCTGAGACACATAGGAGCCTTGGCCGTTGTGGAGTATGCCTACAATGGAAGAGCAG
TCCTGGAGTGGAGGAACCTGCTGACCAGGACCTTTACAGCAATACATTTCAGCTCTACAAGTCAGCAGATCACTCAACCC
TGGACAAAGTATTAGAGGCATACTCAGCAAAACTGGAGCTTATTATGGATGAAATGAAACAGATTTTAACTCCAATGGCC
CAAAAGGAAGCTATGATTAAATACCCATTGGTGCATAAAGTGTTTTTGGACTTTTTCACCTATGCATCCCCCCCAAAACT
AAGATCGGAAATAATTGAAGCCATCCTAGAAGAGGTGGTGTACCTGGCACATAACCATGATGGTGCCACAGTGACCATGC
ACTGCCTCTGGCACAGCACCCCTAAGGATAGGAAAGTGATTGCAAAAACTATGAAAACTTCCTTTCAAAATGTGGCTAAT
GGCCAATACTCCCATTTGGTTTTACCGGCAGCATTTGATTGTATTGACGATACTAAGCTCATGAAGCAGTTAAACATATC
AGAAACTATCATTTCCTTGCCTAGCATAGTAAATGACATATAAGAAAGGAAGGTCCTGTTGTATTTACTGAGCCCCAGAG
ATCCTGCACATACTGTATGAAAAATCATCAAAGTTCTGCTGAAAGGAGATGAAAATGCACGCAGTAAGAGATATACAAAG
ACCTGCTGGCGAGAGCTCTTAGTGACCATCTCCCCAGCTTTGTTAAGCTATCTGCAAGGACACTCCCAAGAGAAAGTGCT
GGATAAGTCTGCGTGTGTGCTGGTGACCGACATCCTGGGATCTGTCTGGGAGACATCTAGCCTGCCATCAATCCCACTAC
CAGCTTGGCAGCAGGCGAGCTGCATCCTGGTGGCTGAGATGAAGAACTTCACTTTGCGGAAGCCCTGTAGGATATCTCAT
TCTGAAGTGACTCACGGAGCAAGACGGAAAGATGAAAGAGAGCTGAAGAGAAGATTATTTTCCAAAAACACTTGTGATGC
ATGATGGGATGAAGAACCTTACATCC

Alignment

ORF - retro_lafr_1029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.32 %
• Parental protein coverage: 67.75 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KRVKLMSDLQKLIQGKIKTIAFAHDSTRVIQCYIQYGNAEQRREAFEELRDNLVE-LSKAKYSRNVVKKF
          .R.KLM.DLQKLIQG.I.T.....DS...IQCYIQY.N.EQR.EAF.EL..NLVE.LSK.KYSR..VKKF
Retrocopy QRKKLMIDLQKLIQGTIETM----DSKCMIQCYIQYRNEEQREEAFKEL*NNLVE>LSKGKYSRKIVKKF

Parental  LMYGSKPQIAEIIRSFKGHVRKMLRHAEASAIVEYAYNDKAILEQRNLLT-EELYGNTFQLYKAADHPTL
          .MY.SKPQIA.IIRS.KGHVRKMLRH..A.A.VEYAYN..A.LE.RNLLT...LY.NTFQLYK.ADH.TL
Retrocopy FMYRSKPQIADIIRSVKGHVRKMLRHIGALAVVEYAYNGRAVLEWRNLLT<QDLYSNTFQLYKSADHSTL

Parental  DKVLEAQPAKLELIMDEMKQILTPMAQKEAVIKHSLVHKVFLDFFTYA-PPKLRSEMIEAIREAVVYLAH
          DKVLEA..AKLELIMDEMKQILTPMAQKEA.IK..LVHKVFLDFFTYA.PPKLRSE.IEAI.E.VVYLAH
Retrocopy DKVLEAYSAKLELIMDEMKQILTPMAQKEAMIKYPLVHKVFLDFFTYASPPKLRSEIIEAILEEVVYLAH

Parental  THDGARVAMHCLWHGTPKDRKVIVKTMKTYVQKVANGQYSHLVLLAAFDCIDDTKLVKQIIISEIISSLP
          .HDGA.V.MHCLWH.TPKDRKVI.KTMKT..Q.VANGQYSHLVL.AAFDCIDDTKL.KQ..ISE.I.SLP
Retrocopy NHDGATVTMHCLWHSTPKDRKVIAKTMKTSFQNVANGQYSHLVLPAAFDCIDDTKLMKQLNISETIISLP

Parental  NIVNDKYGRKVLLYLLSPRDPAHTVREIIEVLQKGDGNAHSKKDTETRRRELLEAISPALLSYLRGHARE
          .IVND...RKVLLYLLSPRDPAHTV..II.VL.KGD.NA.SK..T.T..RELL..ISPALLSYL.GH..E
Retrocopy SIVNDI*ERKVLLYLLSPRDPAHTV*KIIKVLLKGDENARSKRYTKTCWRELLVTISPALLSYLQGHSQE

Parental  MVLDKSACVLVTNILGS-ALGDVQPATSAIASLAAEELHPGGRDGELHVAE-HPAGHLVLKWLIEQDGKM
          .VLDKSACVLVT.ILGS..LGD..PA.....SLAA.ELHPGG.D.ELH.AE..P.G.L.LK.L.EQDGKM
Retrocopy KVLDKSACVLVTDILGS<CLGDI*PAINPTTSLAAGELHPGG*DEELHFAE<SPVGYLILK*LTEQDGKM

Parental  KERSREGCFAKTLVEHVGMKNLKS
          KE..RE..F.KTLV.H.GMKNL.S
Retrocopy KES*REDYFPKTLVMHDGMKNLTS

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_1029 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012187	1 retrocopy	retro_amel_1752,
Callithrix jacchus	ENSCJAG00000010917	1 retrocopy	retro_cjac_2253,
Cavia porcellus	ENSCPOG00000008552	1 retrocopy	retro_cpor_1158,
Loxodonta africana	ENSLAFG00000017341	1 retrocopy	retro_lafr_1029 ,
Mus musculus	ENSMUSG00000041360	1 retrocopy	retro_mmus_3640,
Oryctolagus cuniculus	ENSOCUG00000004189	1 retrocopy	retro_ocun_213,
Sorex araneus	ENSSARG00000000579	1 retrocopy	retro_sara_499,