RetrogeneDB ID: retro_etel_1487

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_273506:3181..3990(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC3
• Ensembl ID: ENSETEG00000002652
• Aliases: None
• Description: voltage-dependent anion channel 3 [Source:HGNC Symbol;Acc:12674]

Sequence

>retro_etel_1487
GCTCGGGATGTCTTCACCAAGGGCTATGCGTCTGCCCTCATAAAACTGGATTGAAGACAAAATCCGAGAATGGACTGGAA
TTTACCAGCTCCGGCTCAGCCAACACCGAGACCAACAAAGTCACGCGCAGTCTGGAAACCAAGTACCGGTGGACCGAGTA
CGGGTTGACATTCACCGAGAAGTGGAACACAGACAACACTCTGGGCACCGAGATCATTGTGGAAGACCAGCTGACCCACG
GACTGAAGCTGACCTTTGACTCGTCCTTCTCCCCAAACACTGGGAAAAAGAACGCCAAAATCAAGACGGGGTACAAGCGG
GAGCACGTCAACCTGGGCTGCGACGTGGATTTTGACATCGCCGGGCCTGCCATCCGCGGGGCCCTGGTGCTGGGCTATGA
GGGCTGGCTGGCTGGCTACCAGATGAACTTCGAGACCGCCAAGTCCCGGGTCACCCAGAGCAACTTTGCGGTTGGCTACA
AGACGGATGAATTCCAGCTTCACACCAATGTGAATGATGGGACAGAGTTTGGCGGCTCCATTTACCAGAAGGTGAACAAG
AAGTTGGAGACTGCTGTCAATCTCGCCTGGACAGCCGGCAATAGCAACACCCGCTTCGGAATAGCAGCCAAGTATCAGAT
CGACCCTGACGCCTGCTTCTCGGCAAAGGTGAACAACTCCAGCCTGATCGGTTTAGGCTACACTCAGACCCTAAAGCCAG
GCATCAAGCTGACACTGTCTGCTCTGTTGGACGGCAAGAATGTCAACGCCGGTGGCCACAAGCTTGGTCTAGGACTGGAA
TTCCAAGCA

Alignment

ORF - retro_etel_1487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.05 %
• Parental protein coverage: 95.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKDVFNKGYGFGMVKID-LRTKSCSGVEFSTSGHAYTDTGKASGNLETKYKVCSYGLTFTQKWNTDNTLG
          A.DVF.KGY.....K.D.L.TKS..G.EF..SG.A.T.T.K....LETKY....YGLTFT.KWNTDNTLG
Retrocopy ARDVFTKGYASALIKLD<LKTKSENGLEFTSSGSANTETNKVTRSLETKYRWTEYGLTFTEKWNTDNTLG

Parental  TEISLENKLAEGLKLTLDTIFVPNTGKKSGKLKASYKRDCFSLGSNVDIDFSGPTIYGWAVLAFEGWLAG
          TEI..E..L..GLKLT.D..F.PNTGKK..K.K..YKR....LG..VD.D..GP.I.G..VL..EGWLAG
Retrocopy TEIIVEDQLTHGLKLTFDSSFSPNTGKKNAKIKTGYKREHVNLGCDVDFDIAGPAIRGALVLGYEGWLAG

Parental  YQMSFDTAKSKLSQNNFALGYKAADFQLHTHVNDGTEFGGSIYQKVNEKIETSINLAWTAGSNNTRFGIA
          YQM.F.TAKS...Q.NFA.GYK...FQLHT.VNDGTEFGGSIYQKVN.K.ET..NLAWTAG..NTRFGIA
Retrocopy YQMNFETAKSRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIA

Parental  AKYKLDCRTSLSAKVNNASLIGLGYTQSLRPGVKLTLSALIDGKNFNAGGHKVGLGFELEA
          AKY..D.....SAKVNN.SLIGLGYTQ.L.PG.KLTLSAL.DGKN.NAGGHK.GLG.E..A
Retrocopy AKYQIDPDACFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_1487 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014068	4 retrocopies	retro_btau_1537, retro_btau_1607, retro_btau_365, retro_btau_685,
Choloepus hoffmanni	ENSCHOG00000007369	1 retrocopy	retro_chof_16,
Echinops telfairi	ENSETEG00000002652	2 retrocopies	retro_etel_1456, retro_etel_1487 ,
Gallus gallus	ENSGALG00000003755	1 retrocopy	retro_ggal_11,
Monodelphis domestica	ENSMODG00000015526	5 retrocopies	retro_mdom_1130, retro_mdom_1331, retro_mdom_1869, retro_mdom_420, retro_mdom_669,
Mus musculus	ENSMUSG00000008892	2 retrocopies	retro_mmus_110, retro_mmus_1505,
Sarcophilus harrisii	ENSSHAG00000017953	1 retrocopy	retro_shar_658,
Tursiops truncatus	ENSTTRG00000009681	3 retrocopies	retro_ttru_1201, retro_ttru_1254, retro_ttru_634,