RetrogeneDB ID: retro_etel_1660

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_286347:74039..74708(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLDN10
• Ensembl ID: ENSETEG00000005415
• Aliases: None
• Description: claudin 10 [Source:HGNC Symbol;Acc:2033]

Sequence

>retro_etel_1660
GTGGTTGCCTTCAGGGTCTCCATCTCCGGCTGGGTGCTGATGTCCTCCACGCTGCCCACCGACTACTGGAAGGTTTCCAC
CATGGACGGCACCGTCATCACCCCCGCCACCTATTGGGCCAACCTGTGGAAGACCTGTGTCACCGACTCCACGGGTGTCT
CCAACTGCAAGGATTTCCCCTGCATGCTGGCGCTGGACGGTTATATCCAGGCATGCGGAGGACTAATGATTGCTGCTGTC
AGCCTTGGCTTTTTTGGTTCCATATTTGCACTGTTTGGAATGAAGTGTACCAAAGTCGGAGGCGCAGATAAAGCCAAAGC
TAAAATTGCTTGTTTGGCTGGAATTGTATTCATACTGTCAGGGCTGTGCTCCATGAACGGCTGTTCCCCATATGCAAACA
AAATCACAACGGAATTCTTCGACCCTCTCTACATTGAGCAAAAGTCTGAGCTAGGAGCTGCTCTGTTCATTGGATGGGCG
GGAGCATCACTCTGCATAATTGGTGGTGTCCTATATTGCTTCTCAGAATCTGACAACAACAAAACACCCAGAATGGGATA
TGCATACAATGGGGCCATATCAGTCCTGTCTTCTCGGACCAAGTACCACGGTGGAGAAGGAGACTAAAACCACAACCCTT
CCAAACAGTTTGATAAAAATGCTTATGTG

Alignment

ORF - retro_etel_1660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.39 %
• Parental protein coverage: 96.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IIAFMVSISGWVLVSSTLPTDYWKVSTIDGTVITTAT--ANLWKTCVTDSTGVSNCKDFPSMLALDGYIQ
          ..AF.VSISGWVL.SSTLPTDYWKVST.DGTVIT.AT..ANLWKTCVTDSTGVSNCKDFP.MLALDGYIQ
Retrocopy VVAFRVSISGWVLMSSTLPTDYWKVSTMDGTVITPATYWANLWKTCVTDSTGVSNCKDFPCMLALDGYIQ

Parental  ACRGLMIAAVSLGFFGSIFALFGMKCTKVGGSDKAKAKIACLAGIVFILSGLCSMTGCSLYANKITTEFF
          AC.GLMIAAVSLGFFGSIFALFGMKCTKVGG.DKAKAKIACLAGIVFILSGLCSM.GCS.YANKITTEFF
Retrocopy ACGGLMIAAVSLGFFGSIFALFGMKCTKVGGADKAKAKIACLAGIVFILSGLCSMNGCSPYANKITTEFF

Parental  DPLYVEQKYELGAALFIGWAGASLCIIGGVIFCFSISDNNKTPR--YAYNGATSVLSSRTKYHGGEGDFK
          DPLY.EQK.ELGAALFIGWAGASLCIIGGV..CFS.SDNNKTPR..YAYNGA.SVLSSRTKYHGGEGD..
Retrocopy DPLYIEQKSELGAALFIGWAGASLCIIGGVLYCFSESDNNKTPRMGYAYNGAISVLSSRTKYHGGEGD-*

Parental  TTTPSKQFDKNAYV
          ...PSKQFDKNAYV
Retrocopy NHNPSKQFDKNAYV

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_1660 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003817	1 retrocopy	retro_cpor_1378,
Echinops telfairi	ENSETEG00000005415	1 retrocopy	retro_etel_1660 ,