RetrogeneDB ID: retro_lafr_1163

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:63903865..63904680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BIN2
• Ensembl ID: ENSLAFG00000002387
• Aliases: None
• Description: None

Sequence

>retro_lafr_1163
GTGGCCATCTTCCAAAACATTTCCAACCTAAGGGATGTTTTCTACAGAGTTATGAGCAAGCTGAACCGCAATCTCTATGA
GGTGATGAGCAAACTGGAGGAACAACATTCCAACAAAGTCTTTGTGGTGAAAGGACTATCAAGCAGCAGTAGATGGTCTT
TGGTCATCTCTCCCCCAGTTCGAGCATCTACAGTCTCCAGTCCTCTCACCTCACCTACCAGCTCCTCTGTACTTTTCTTA
AAGAGTGAGAAGGAATCCATTTCAGCAGCTGAAGAAGAGCTGACACCTGATCCAGCCCAGGGAGAAGACAACTCTAGATC
AAAGAAGAACCCTTAAAAGATGAGGAAATAGAAGGGGGAGAGGCCAAAGCCTGCTCCTTTAAGGAAGAAGAACTTCTGCC
AATCTACAATGGCCCAACCCAAACCCAGCTCTCTCCCAACATTGAGGGTGGTGATTCCCAGGAGGAAATTTTCTCTTGCT
CCCCAGCTCCATCACCAGGCAGAGCCCTAACCCCTTCAGAGCAGCCTTCATCATCTCTTCCAGAAGTAGTCCTCTGAACC
TGCACAAGTGAAGGGTCTGAACAACCAAAGAAAAGAGCCTCTCTCTCAAGGACCTCAGAGCCCCCTAGTAGGCCTCCTCC
ACCCAGAGCCACTCCTAGCCCCAGGCTTTCTTCAGGGAACATACCCTTCAGCCCTACTCCCTCTGAAGGAGGTTCACCCA
CCAACCCTAGGGGCTTCTTGAGGGTTGGTACTCCCAGTCCTAGGGCCTCCATACAGGCATCTCCTCATCCAGAGCCTTCA
GAGAAGCCAGATAGA

Alignment

ORF - retro_lafr_1163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.29 %
• Parental protein coverage: 56.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTIFQNISNLKDVFYREMSKLNHNLYELMSKLEKQHSNKVFVVKGLSSSTKRSLVISPPVRKSTVSSPLT
          V.IFQNISNL.DVFYR.MSKLN.NLYE.MSKLE.QHSNKVFVVKGLSSS...SLVISPPVR.STVSSPLT
Retrocopy VAIFQNISNLRDVFYRVMSKLNRNLYEVMSKLEEQHSNKVFVVKGLSSSSRWSLVISPPVRASTVSSPLT

Parental  SPTSPSALSLKSERESISAAEEELAPDPAQGEDNSE-IKEEPLKDEEIEGGGAKTSSSEEEEPLPAYNGP
          SPTS.S.L.LKSE.ESISAAEEEL.PDPAQGEDNS..IKEEPLKDEEIEGG.AK..S..EEE.LP.YNGP
Retrocopy SPTSSSVLFLKSEKESISAAEEELTPDPAQGEDNSR<IKEEPLKDEEIEGGEAKACSFKEEELLPIYNGP

Parental  TQTQPSPTIEGGESQEEVFSCSPAPASGRALNPSEQTSPSLPVVVLRTRTTSEGSEQPEKKASLSRTSAP
          TQTQ.SP.IEGG.SQEE.FSCSPAP..GRAL.PSEQ.S.SLP.VVL.T..TSEGSEQP.K.ASLSRTS.P
Retrocopy TQTQLSPNIEGGDSQEEIFSCSPAPSPGRALTPSEQPSSSLPEVVL*T-CTSEGSEQPKKRASLSRTSEP

Parental  PSRPPPPRASPRLRHSSGSIPSSPTASEEGSPTRPRAFLGAGTPSPRASIQASPDPEPSEKPER
          PSRPPPPRA.P..R.SSG.IP.SPT.SE.GSPT.PR.FL..GTPSPRASIQASP.PEPSEKP.R
Retrocopy PSRPPPPRATPSPRLSSGNIPFSPTPSEGGSPTNPRGFLRVGTPSPRASIQASPHPEPSEKPDR

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_1163 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110934	2 retrocopies	retro_hsap_2952, retro_hsap_3192,
Gorilla gorilla	ENSGGOG00000009423	1 retrocopy	retro_ggor_1336,
Loxodonta africana	ENSLAFG00000002387	1 retrocopy	retro_lafr_1163 ,
Nomascus leucogenys	ENSNLEG00000017774	1 retrocopy	retro_nleu_1636,
Pongo abelii	ENSPPYG00000004526	2 retrocopies	retro_pabe_2448, retro_pabe_2648,
Pan troglodytes	ENSPTRG00000004954	2 retrocopies	retro_ptro_2049, retro_ptro_2251,