RetrogeneDB ID: retro_etel_779

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_163215:3659..4779(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSETEG00000004811
• Aliases: None
• Description: SDA1 domain containing 1 [Source:HGNC Symbol;Acc:25537]

Sequence

>retro_etel_779
GTGTTTGTGGCACAGAATGGACACTGCTACCCAGAACAGCTCAGTAGCTTTCCTCAGGAATGGAAAGATCTACTCTCCTA
CTGTCACACTGTCTTGGATCCTGATCTTCGAATGACATTGTGCAAAGCTTTGATCTTATTGAGAAGCAAGCATCTCATCA
ACCCATTGAGTTTGCTCGAGCTCTTCTTTGCACTTCTGTGTTGCCATGATACGCGTCTGTGAAAGACTTTGTACACTCAC
ATTGTGACTGATATCAAGAACATAAATGAAAAGCACGAGAGCAATAAAGTGAATGTAGTGCTGCAACACTTCATGGACCC
CGTGCTCAGGGATCGCCATGCAATGGCAGCTAAGATCTCCTTGGATGTGAGGATTGAACTCTACAGAAGAAACATCTGGA
ATGATGCCCAAACTGTCAGTTACCACAACGACATGCTTATCTCTGGTCACCAAGATACTGGTGGCTGCTTTGACATTCTT
CCTCGGGAAAGATGAGCAGGAGAAGCAGGACAGCGACTCGGACTCGGAGGATGAAGAGCCAACCGCGAGAGACCTCCTCG
TGCAGTACGCCACGGGGAAGAAAAGCTCCAAGCACAAGAAGAAACTGGAGAAGGCCATGAAGGTGCTCAAGAAACAAAAG
AAGAAGAAGAAACCGGAGGTGTTTAACTTCTCAGCCATTCACTTGATTCATGATCCCCAAGATTTTGCTGAAAAACTACT
GAAACAACTCGAGAGCTCCAAGGAGAGATTTGAAGTGAAGATGATGCTCATGAACCTTATCTCCAGATTGGTGGGAATTC
ATGAGCTCTTCCTCTTTAACTTCTATCCCTTCGTTCAAAGGTTTCTGCAGCCCCACCAGAGAGAAGTCACAAAGATCCTT
CTGTTTGCTGCACAAGCCTCTCATCACCTGGTTCCCCCGGAGATCATTCAGTCATTGCTCATGACGGTGGCCAACAATTT
TGTCACTGACAAGAACTCTGGAGAAGTTATGACCGTAGGAATCAATGCCATCAAAGAGATAACAGCTCGATGTCCCCTAG
CCATGACTGAAGAACTTCTCCAAGACCTGGCTCAGTATAAAACACACAAAGATAAGAATGTGATGATGTCTGCTAGAACT

Alignment

ORF - retro_etel_779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 59.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFMAQIGHCYPEQLSSFPQELKDLLSYNHTVLDSDLRMTFCKALILLRNKNLINPSSLLELFFELLRCHD
          .F.AQ.GHCYPEQLSSFPQE.KDLLSY.HTVLD.DLRMT.CKALILLR.K.LINP.SLLELFF.LL.CHD
Retrocopy VFVAQNGHCYPEQLSSFPQEWKDLLSYCHTVLDPDLRMTLCKALILLRSKHLINPLSLLELFFALLCCHD

Parental  KLLRKTLYTHIVTDIKNINAKHKNNKVNVVLQNFMYTMLRDSSATAAKISLDVMIELYRRNIWNDAKTVN
          ..L.KTLYTHIVTDIKNIN.KH..NKVNVVLQ.FM...LRD..A.AAKISLDV.IELYRRNIWNDA.TV.
Retrocopy TRL*KTLYTHIVTDIKNINEKHESNKVNVVLQHFMDPVLRDRHAMAAKISLDVRIELYRRNIWNDAQTVS

Parental  -VITTACFSPVTKILVAALTFFL-KDEQEKQDSDSDSE-EGPTARD-LVQYATGKKSSKHKKKLEKAMKV
          ...TT.C.S.VTKILVAALTFFL.KDEQEKQDSDSDSE.E.PTARD.LVQYATGKKSSKHKKKLEKAMKV
Retrocopy >TTTT-CLSLVTKILVAALTFFLGKDEQEKQDSDSDSEDEEPTARDLLVQYATGKKSSKHKKKLEKAMKV

Parental  LKKQKKKKKPEVFNFSAIHLIHDPQDFAEKLLKQLESSKERFEVKMMLMNLISRLVGIHELFLFNFYPFV
          LKKQKKKKKPEVFNFSAIHLIHDPQDFAEKLLKQLESSKERFEVKMMLMNLISRLVGIHELFLFNFYPFV
Retrocopy LKKQKKKKKPEVFNFSAIHLIHDPQDFAEKLLKQLESSKERFEVKMMLMNLISRLVGIHELFLFNFYPFV

Parental  QRFLQPHQREVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAM
          QRFLQPHQREVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAM
Retrocopy QRFLQPHQREVTKILLFAAQASHHLVPPEIIQSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAM

Parental  TEELLQDLAQYKTHKDKNVMMSART
          TEELLQDLAQYKTHKDKNVMMSART
Retrocopy TEELLQDLAQYKTHKDKNVMMSART

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_779 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008521	2 retrocopies	retro_cfam_1211, retro_cfam_515,
Echinops telfairi	ENSETEG00000004811	2 retrocopies	retro_etel_1946, retro_etel_779 ,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Microcebus murinus	ENSMICG00000006682	1 retrocopy	retro_mmur_1204,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Sus scrofa	ENSSSCG00000008974	1 retrocopy	retro_sscr_571,