RetrogeneDB ID: retro_lafr_899

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_46:8729950..8731024(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CABYR
• Ensembl ID: ENSLAFG00000014928
• Aliases: None
• Description: None

Sequence

>retro_lafr_899
TTAAAAAAAAAAAAAAAAAAGGTCACCCAGTTCACTGTTATTTATTTTAAAGAACTTATTTTGTTTCAAGAAGGAAACAC
TTCCATGGATATAAAAGAACTGGTTAAACAATTTCATCAGATTAAAGTTGAGAAGTGGTCAGAAAGAACAACACAAGAGA
AGAAACCAGAATGTGTAAAAGAATGAGAAAGAGCATCTGTAATTTCTCCAGAACTTACATGGAAGGAAAAATCTACAGAC
TCAGAGGAGGACAATATATCTTGACCACTATTTTGCAACAAAACCAGCTAGTTTCCATCAGTTCTTGCTGAACTCCCAGA
GCACGTGAACATACCTAAAACAGTTTGTGGTTCTTCCAAATCATCCATTCCTAAGGTTACCACCTCACCCTCATTAACAT
CTCCAGCAGCTGTCCCACCAGAGTTTGCCTATGTCCCAGCTGACCCAGCTCTGTTTGCTGCCCAGATGTTAGCAATAGCA
GCAAGTGAAGCAGGACAACCACCACCGTATTCTAACATGCAGACCTTTTATTGTCTAGCTGATATGAATCAACAAAGTAA
CCCGTCACCACCACCTGCAGCTGGTCCTTTTCCTCAAGCAAACTTGTATTTATCTAATTCTAGGAATCCACAGTTTCTGC
AGCATCCAACTTCTGCAGCATAAGTTACTTCTCCAACTTATGTGATGATGAATGACACCAAGAAGACCGGTGCCCAACCT
TTTATTTTAGTAGGCTCAAATGTTCAGGAAGCACAGAATCGGAAACCTCTTCCTGGACATGCTGTTGTTTCACAGTCAGA
TATCTTGAAGGGATATGCTGCAGTATAATACCCATTGTTGTTCTTGCAGGTGAGAAACTCCAGAAACACACCCTAAATTC
CCAGAATGCTAGTCATCCTACAAGTGGACAAGATGTCACTTAACAACAAAGCCCAGTTTTTCTTTCTGTTGCTTTCCCAG
TAGAGGATGTAGCCAAAAAAGTTCAAGATCTGGGACAAACTTAGTCCCTTTGGAAGTTACAGTATTGCTGGAGAAATTAC
CATGACTACTGCCCATGTTTGCAGAGCAAAAACT

Alignment

ORF - retro_lafr_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.41 %
• Parental protein coverage: 93.46 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKTNPANITQFAAIYFKELILFREGNTSMDIKELVKQFHQIKVEKWSEGTIQEKKPECVKEPERASVIPP
          LK......TQF..IYFKELILF.EGNTSMDIKELVKQFHQIKVEKWSE.T.QEKKPECVKE.ERASVI.P
Retrocopy LKKKKKKVTQFTVIYFKELILFQEGNTSMDIKELVKQFHQIKVEKWSERTTQEKKPECVKE*ERASVISP

Parental  EPTRKEKSTDTEEDNIAKPLFSNKTTQFPSVHAELSEHVDVPEIVSGSSSKPSTPKVTTPPSSPSPAAVP
          E.T.KEKSTD.EEDNI..PLF.NKT..FPSV.AEL.EHV..P..V.G.SSK.S.PKVTT.PS..SPAAVP
Retrocopy ELTWKEKSTDSEEDNIS*PLFCNKTS*FPSVLAELPEHVNIPKTVCG-SSKSSIPKVTTSPSLTSPAAVP

Parental  PEFAYVPADPAQFAAQMLAIAASEAGQPPPYSNMWTLYCLADMNQQSRPSPPPAPGPFPQATLYLSNPKD
          PEFAYVPADPA.FAAQMLAIAASEAGQPPPYSNM.T.YCLADMNQQS.PSPPPA.GPFPQA.LYLSN...
Retrocopy PEFAYVPADPALFAAQMLAIAASEAGQPPPYSNMQTFYCLADMNQQSNPSPPPAAGPFPQANLYLSNSRN

Parental  PQFLQHPPK---VTSPAYVMMDDTQKTGAPPFILVGSNVQEAQDWRPLPGHAVVSQSDTLKRYAAV-QVP
          PQFLQHP.....VTSP.YVMM.DT.KTGA.PFILVGSNVQEAQ...PLPGHAVVSQSD.LK.YAAV...P
Retrocopy PQFLQHPTSAA*VTSPTYVMMNDTKKTGAQPFILVGSNVQEAQNRKPLPGHAVVSQSDILKGYAAV<IIP

Parental  IAVPADQKFQKHTPNAQNASPPPSGQDAPRPQSPVFLSVAFPVEDVAK-KSSGSG-DKRTPFGSYGIAGE
          I.V.A..K.QKHT.N.QNAS.P.SGQD....QSPVFLSVAFPVEDVAK.KSS.SG.DK..PFGSY.IAGE
Retrocopy IVVLAGEKLQKHTLNSQNASHPTSGQDVT*QQSPVFLSVAFPVEDVAK<KSSRSG<DKLSPFGSYSIAGE

Parental  ITVTTAHVRRAET
          IT.TTAHV.RA.T
Retrocopy ITMTTAHVCRAKT

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_899 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020641	1 retrocopy	retro_cjac_1459,
Cavia porcellus	ENSCPOG00000008281	1 retrocopy	retro_cpor_1541,
Loxodonta africana	ENSLAFG00000014928	1 retrocopy	retro_lafr_899 ,