RetrogeneDB ID: retro_lafr_1143

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_77:1727456..1728586(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TEAD2
• Ensembl ID: ENSLAFG00000016184
• Aliases: None
• Description: None

Sequence

>retro_lafr_1143
GGCACGAGCCGCAGGGAGGGGGCTGGGTGAGATGGCCCAGATGTGGAAAGTGTCTGGAACCCAGACATCAAGGAAAGTTT
CCAGGAAACCCTGGCTATCTATCCACCCTGTGGTCAGTGGAAGATCATCCTGTTCGATGAAGGCAAGATGTATGGTGAGA
ATGAACCATTTGCCCACTATATCAAGCTCAGAACCAGGAAGACCCAAACTTGCAAACAGGTCTCTACTCACATCTAGGTT
TTGGCCCAAAGGAAATTGAGAGAAATCCAGTCCAAGCTCAAGGACCACGTTTCCAAGGACAAGGCTTTCCAGAAAATGAC
CACCATGTTCTCAGTCCAGCTCATCTCAGCACATTCCCTGCAGGCCAAACTGGGTCCCACAGGCCTTCAGGCTTCTGAGA
TTTTCCAGTTTGGATCAGGGGGTCTGGGGCCCCTGGAATATTCCAGACGTGAAGTCATTCTCAAAGATGCCGTTCTCCTT
GTCTCTGCCTCCCCATCCGCTGACCTCCCAGGGTACAAGCCCCCGCAAGCCCTCTCACTCACGGCCCTGCCCCCACCTGC
ATGTCACCCGCAGCCTGGCAGGCTCGGCTGTGGGCACTACCCAGTTGCAGCTGGTGGAGTTCTCAGCCTTTGTAGAACCG
CTGGATGCTGTTGGCTCTTACCAGAGGCACCCATTCCTACACATCAGCTCACACTGCCCCAGCCCCGGAGCTCGCCCACT
TGAGAGCATGGACGTCCAGCAGACCTCCGACAAATTCCCCAAGAAAAAGGGCTGTCTGAGGGAGCTATATGATTGTACAC
CCTCTCATGCCTTTTTCCTGGTCAAGTTCTGGGTGGACATGAATTGCGGCCCAAGTGGTGAGCAGATGGGTGGGTGCCAG
TGGCAGCAGCTTCTACAGACTGAGCAGCCGGTATGAGAGCCTAGGGCACATGACCCTCACCTGTTCCTCCAAGAGCTGCT
CCTCTGGCAAGCTGGTGGTGGAGATGGGAGATAAGGAGCATGCGAAGCTAGAGGACGAGTGGTTCGTGTACTGCCTGCTG
TGCTTGTCCATGTGTAAGTGCCTGGTGAACTTCTTGCACAAGCTGCAGCAGCTGCCCAGGTGGTACATGATGAACAGCAT
CCTGGAGCAT

Alignment

ORF - retro_lafr_1143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.91 %
• Parental protein coverage: 84.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GTGGSEGAGGDGGPDAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTR
          GT...EGAG.DG.PD.E.VW.PDI..SFQE.LAIYPPCG..KIIL.DEGKMYG.NE..A.YIKLRT.KT.
Retrocopy GTSRREGAG*DG-PDVESVWNPDIKESFQETLAIYPPCGQWKIILFDEGKMYGENEPFAHYIKLRTRKTQ

Parental  TRKQVSSHIQVLARRKSREIQSKLKDQVSKDKAFQTMATMSSAQLISAPSLQAKLGPAGPQAAEIFQFWS
          T.KQVS.HI.VLA.RK.REIQSKLKD.VSKDKAFQ.M.TM.S.QLISA.SLQAKLGP.G.QA.EIFQF.S
Retrocopy TCKQVSTHI*VLAQRKLREIQSKLKDHVSKDKAFQKMTTMFSVQLISAHSLQAKLGPTGLQASEIFQFGS

Parental  G-GSGTP-WNVPDVKPFSQTSFSLSLTP-PSTDLPGYEPPQALSLPDLPPPA-PSPPAWQTR-ALGTARL
          G.GSG.P.WN.PDVK.FS...FSLSL.P.PS.DLPGY.PPQALSL..LPPPA..SP.AWQ.R.A.GT..L
Retrocopy G<GSGAP<WNIPDVKSFSKMPFSLSLPP<PSADLPGYKPPQALSLTALPPPA<MSPAAWQAR<AVGTTQL

Parental  QLVEFSAFVEPPDAVDSYQRHLFVHISQRCPSPGAPPLESVDVRQIYDKFPEKKGGLRELYDRGPPHAFF
          QLVEFSAFVEP.DAV.SYQRH.F.HIS..CPSPGA.PLES.DV.Q..DKFP.KKG.LRELYD..P.HAFF
Retrocopy QLVEFSAFVEPLDAVGSYQRHPFLHISSHCPSPGARPLESMDVQQTSDKFPKKKGCLRELYDCTPSHAFF

Parental  LVKFWADLN-WPS-VRAGAGGSSGGFYGVSSQYESLEHMTLTCSSKVCSFGKQVVEKVETERAQLEDGRF
          LVKFW.D.N..PS.V....G.S...FY..SS.YESL.HMTLTCSSK.CS.GK.VVE....E.A.LED..F
Retrocopy LVKFWVDMNCGPS>VSRWVGASGSSFYRLSSRYESLGHMTLTCSSKSCSSGKLVVEMGDKEHAKLEDEWF

Parental  VYRLLRSPMCEYLVNFLHKLRQLPERYMMNSVLEN
          VY.LL...MC..LVNFLHKL.QLP..YMMNS.LE.
Retrocopy VYCLLCLSMCKCLVNFLHKLQQLPRWYMMNSILEH

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_1143 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000016184	1 retrocopy	retro_lafr_1143 ,
Otolemur garnettii	ENSOGAG00000010067	2 retrocopies	retro_ogar_2638, retro_ogar_3448,
Rattus norvegicus	ENSRNOG00000020695	1 retrocopy	retro_rnor_1929,