RetrogeneDB ID: retro_etel_534

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_8871:2551..3918(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000015854
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PNN
• Ensembl ID: ENSETEG00000009975
• Aliases: None
• Description: pinin, desmosome associated protein [Source:HGNC Symbol;Acc:9162]

Sequence

>retro_etel_534
CCAGCGTTGCAGTCTTTAGTTGTAGCTACTTCCAAAGAGTGAACATGCAGAGACCTTATCCAGGATGAAAACATGGATGC
AAAGGGAAAACAAAGGAATCGACGGATATTTGGCTTGTTGATAGGCACACTTAAGAAATGTAAACAAGAATCCACTGTTG
CTCAATGAAAAGCAAAAGAGATGACAGGAAATTGAACAAAAGCTTGAAGTGCAGGGCAGAAGAAGAGAGAAAAACAGGTC
GAAAATGAGAGGGCGAGCACTGTTTGGAGGAGAGGTGTGCTAAACAGAACTGCGGCGTTTAGAACAGAAAGTTGAGCTCT
TGTGCAGCTGCAAGAAGAATGGAATGAGCATAATGCCAAGATAATTAAATATATAAGCACTAAAACAAAGCCCCATTTGT
TCTATATTCCTGGAAGAATGTGTCCAGCTACCCAAAAACTAATAGAAGAGTCACAGAGAAAAATGAATGCTTTACTTGAA
GGTAGACGCATCGAATTTGCAAAACAAATAAATAAAATGGAAGCTAGGCCTAGAAGACATTCAATGAAGGAAAAGAGCAT
CAGGTGGTGTGTCATTAAGAACAGAAGGCGGAACAAGAAGAGGGTAAGATGGCTCAGCGTGAGGAAGAATTGGAGACAGG
TAATCAGCACAATGATGTAGAAATAGAGGAAGCAGGAGAGGAAGAGGAAAAGGAGTAGGTATAGTTCATAGTGATACGGA
AAAAGAACAGGAGGAGAAGTAAAAACGGGAAATAGAGGTTAAGGTGGAGAAAGTAATTGAGGCAAGGGAAAGTGAAAAGT
AGCAGGATTGTCAGCCTGAAGAAGTTAGGATGTGGTAGAGATGGTTGAAAATGTCAAAAATGTAATTGTTGAGCAGGAGA
CAATGGAAACAAATCAAGTTGAAAGTACAGAACCTTCAGAAAATGAAACTAGCAAAGAAATGGAGCCAGAGATGGAGTTT
GAAGTTGAACCAGAAAAAGAATGTAATTCTTTCTCCTGCGAAACAGAATAGTACTAGCGTTGTAGAAATAGAAAAGGAGC
TTGAGGAAAATGAAGGAAAGGAATCTGAGCTCCAACCAGAGCCAATCACTCAACCTCCACCCCAAATCCAATCTCAGTCC
CAATCCCAACCCCAGCCAATACTTCAGCCCCCACCTCTTTCTCAGCCTGAGGCTTTGCAATTGAGTTTCACAGCCACCAC
CTCAGGTTTTCCAGGAGCAAGGGCATTCACTACCTGAGAGGAAGGAATTTCCTGTAGAATCTGTGAAACTCAGTGAAGTG
CCACCAGAGCCAGTCTTGACAGTGCACATAGACAACAAAGGCAAAACCAAAACTAGGAGCCGAAGCAGAGGTCTGGCTAG
AAATAAA

Alignment

ORF - retro_etel_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.25 %
• Parental protein coverage: 64.06 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  PALQSSVVATSKERTRRDLIQDQNMDEKGKQRNRRIFGLLMGTLQKFKQESTVA-NEKQKRRQEIEQKLE
          PALQS.VVATSKE.T.RDLIQD.NMD.KGKQRNRRIFGLL.GTL.K.KQESTVA.NEKQKR.QEIEQKLE
Retrocopy PALQSLVVATSKE*TCRDLIQDENMDAKGKQRNRRIFGLLIGTLKKCKQESTVA>NEKQKR*QEIEQKLE

Parental  VQ-AEEERK-QVENERRELFEERRAKQTELRLLEQKVELAQLQEEWNEHNAKIIKYIRTKTKPHLFYIPG
          VQ.AEEERK.QVENER......R...............L.QLQEEWNEHNAKIIKYI.TKTKPHLFYIPG
Retrocopy VQ>AEEERK>QVENERASTVWRRGVLNRTAAFRTES*ALVQLQEEWNEHNAKIIKYISTKTKPHLFYIPG

Parental  RMCPATQKLIEESQRKMNALFEGRRIEFAEQINKMEARPRRQSMKE-KEHQVVRNEEQKAEQEEGKMAQR
          RMCPATQKLIEESQRKMNAL.EGRRIEFA.QINKMEARPRR.SMKE.KEHQVV...EQKAEQEEGKMAQR
Retrocopy RMCPATQKLIEESQRKMNALLEGRRIEFAKQINKMEARPRRHSMKE<KEHQVVCH*EQKAEQEEGKMAQR

Parental  EEELEETGNQHNDVEIEEAGEEEEKE-VGIVHSDPEKEQEEEEQKQEIEVKVEEEMGARESEKQQDSHPE
          EEEL.ETGNQHNDVEIEEAGEEEEKE.VGIVHSD.EKEQ.EE..K.EIEVKVE....ARESEK.QD..PE
Retrocopy EEEL-ETGNQHNDVEIEEAGEEEEKE<VGIVHSDTEKEQ-EEK*KREIEVKVEKVIEARESEK*QDCQPE

Parental  EVM-DVLEMADNAKHAIVEQETMETNQVESIEPSENETSKEMEPEMEFEVELDKECKALSPAKE-NSTSV
          EV..DV.EM..N.K..IVEQETMETNQVES.EPSENETSKEMEPEMEFEVE..KEC...S...E.....V
Retrocopy EVR<DVVEMVENVKNVIVEQETMETNQVESTEPSENETSKEMEPEMEFEVEPEKECNSFSCETE>STSVV

Parental  VEIEKEPEENEKESEPQPEPINQPPPQIQSQSQSQPQPTLQPPPLSQPEALQLTVS-QPPPQVIQEQGHS
          .......E...KESE.QPEPI..................LQPPPLSQPEALQL.....PP.QV.QEQGHS
Retrocopy EIEKELEENEGKESELQPEPITXXXXXXXXXXXXXXXXILQPPPLSQPEALQLSFT>PPP-QVFQEQGHS

Parental  LPERKEFPVESVRLSEVPPEPVLAVLVDSKGKTKTRSRSRGRARNK
          LPERKEFPVESV.LSEVPPEPVL.V..D.KGKTKTRSRSRG.ARNK
Retrocopy LPERKEFPVESVKLSEVPPEPVLTVHIDNKGKTKTRSRSRGLARNK

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_534 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009975	1 retrocopy	retro_etel_534 ,
Rattus norvegicus	ENSRNOG00000004061	1 retrocopy	retro_rnor_1225,