RetrogeneDB ID: retro_etel_194

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_3340:344963..345505(+)
• Located in intron of: ENSETEG00000014638

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCAP29
• Ensembl ID: ENSETEG00000008025
• Aliases: None
• Description: B-cell receptor-associated protein 29 [Source:HGNC Symbol;Acc:24131]

Sequence

>retro_etel_194
ACTTTTGGGGACAAGGCTTTCCTTACTACTGTATTCCTATTGATTGTTCTGTTTCTGGATGCTGTGAGAGAAATAAGAAA
ATATTCCTGTACTCATAGCATTGAGAAGAGTTCAGCCAGTAAACCTAATGCCTGTGGACATACACAAATGAAACTTTTTA
GGTCTCAAAGAAATATTTACATTTCTGGATTTTCATTATTTTTTGGCTTGAGGTGTGCTTACTCTCATTACTTCAACTAA
CAAAATAATTGCCAACCAAAGTAGTACTTAAAACATAAACAAAATACTAGCAAGGCTGCCAAAAAATTCATGGAAGAGAA
TGAAAATCTAAAACAGATCATAAAAAATTATGGAAAGGGAGAGCAACAGATGTGTGGAAGAAGACAATAGAAAACTAGTA
GAGGACCAGGGAAAACTGAAAATTGAAAGAAGACTACACGTGGCCTTTTCTAAAGTACAAATTGACATAGTTACAAGCCA
GGGCACACAGAGACTTTCTGTAGGGATATGACCAGCTCCTGAAAGAGCATTCAGACCATCAA

Alignment

ORF - retro_etel_194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.43 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TFLNKAFLTIIVLLIVLFLDAVREIRKYSFAHSMQKSSAGRPSAYDHTQMKLFRSQRNLYISGFSLFF-W
          TF..KAFLT...LLIVLFLDAVREIRKYS..HS..KSSA..P.A..HTQMKLFRSQRN.YISGFSLFF.W
Retrocopy TFGDKAFLTTVFLLIVLFLDAVREIRKYSCTHSIEKSSASKPNACGHTQMKLFRSQRNIYISGFSLFF<W

Parental  LVLRRLVSLITQLAKELSTKGV-LKIQTENTTKAAKKFMEENEKLKQVMKNYGKGEQPI-LEAENEKLVE
          L....L.SL..QL.K.L.TK.V.LK....NT.KAAKKFMEENE.LKQ..KNYGKGEQ....E..N.KLVE
Retrocopy LEVC-LLSLL-QLTK*LPTKVV>LK-HKQNTSKAAKKFMEENENLKQIIKNYGKGEQQM>VEEDNRKLVE

Parental  DREKLKTELKKTTDALSKAQNDVMAMKMQSERLSK-EYDRLLKERSELQ
          D..KLK.E......A.SK.Q.D.........RLS...YD.LLKE.S..Q
Retrocopy DQGKLKIE-RRLHVAFSKVQIDIVT-SQGTQRLSV>GYDQLLKEHSDHQ

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_194 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016329	1 retrocopy	retro_cjac_2669,
Echinops telfairi	ENSETEG00000008025	1 retrocopy	retro_etel_194 ,
Echinops telfairi	ENSETEG00000008662	1 retrocopy	retro_etel_1522,
Oryctolagus cuniculus	ENSOCUG00000027511	1 retrocopy	retro_ocun_235,
Otolemur garnettii	ENSOGAG00000013116	1 retrocopy	retro_ogar_2169,