RetrogeneDB ID: retro_etel_2103

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_59969:558..1558(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLHL12
• Ensembl ID: ENSETEG00000007800
• Aliases: None
• Description: kelch-like family member 12 [Source:HGNC Symbol;Acc:19360]

Sequence

>retro_etel_2103
ATGCAGTTGGGTTCTGAAGAGCCCATCTTTGAAGCTGTCATCAACGAGGCGCAGCGTGCCAAGGAGGGAGAAGAATCTTT
ACCTGACCTGCTACAATACATCCAGATGCCCCTGCTGACGCCCAGGGGCATCGTGGATGTTACAGACGCTCAGACTTGGA
TCCAGTGCAGTTTTCAATGCAGAGATCTAACTGGTGAAGCAAGGTTTCCTCTGAGGCCTGAACTGCAGTCAGATTCAGGG
AGCCAGACTCAGGACATGTCCAGGAACCAATGAAGTACTGCTGGTGGTTGAGGGCTTAGAAACCAGCATTCTCCCATTGA
TGGGGTAGAGAAATACAACCCAAAACTCAGGAGTGGAGCTTTTAGGCAAGCATTACTCTTAAGAGGTGCTCGGTCTACCT
ACATGACTGGATCTGTGTAATGGGTGGCTATGATGGCCATTCCCACTTCAGTTCAGTGGACTGTCTAGACTACCCAGCAG
ATGAGGTTGGGGTCTGGTATTCTGTTACTCCTAGAAATGTTTTATGAGCTCTCACTGGACCCACTACCCTAGGAGATAAG
ATTTGTGTCCCTGGAGGCCTTGATACAACCACTTATCCTACCATTACAGAGAGATGGGACCCCAACATTGATCAGTGGAG
CATTCTGGGAGATATGTAGACATCCTGGGAAGGTTCAGGACCTGTGGTAGCCAGTGGGTTGATCTGTCAGGGAGGATATT
ATGGATATGGTGGCTTGAATATCTTAAACTCAGTCGATAAATATCCTCACACAGGTCAGTAGACTAATGTCACACAGATG
GCCACCAAGCCTTCTGGTGCAGGAGGAGCCCTGCTAAATGACCATATTTATGTGTAGAGGGGACTTGATGGTATAGGCCA
CCTCTCTTCTGTTGAAGCGTACAACATTCATACTGATTCTTGGAAATTGGCGCCAATATGACTACCCCATGATGCTATGT
AGGGGCTTCAGTGCTGCAGGGGAGACACTGTGCAATTGCA

Alignment

ORF - retro_etel_2103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.9 %
• Parental protein coverage: 68.48 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IQVDSEEPVFEAVINWVKHAKKEREESLPDLLQYVRMPLLTPRYITDVIDAEPFIRCSLQCRDLVDEAKK
          .Q..SEEP.FEAVIN....AK.E.EESLPDLLQY..MPLLTPR.I.DV.DA...I.CS.QCRDL..EA..
Retrocopy MQLGSEEPIFEAVINEAQRAK-EGEESLPDLLQYIQMPLLTPRGIVDVTDAQTWIQCSFQCRDLTGEA-R

Parental  FHLRPELRSQMQGPRT-RARLGANEVLLVVG-GFGSQQSPIDVVEKYD-PKTQEWSFLPSITRKRRYVAS
          F.LRPEL.S...G..T.R...G.NEVLLVV..G...Q.SPID.VEKY..PKTQEWSF..SIT.KR....S
Retrocopy FPLRPELQSD-SGSQT>RTCPGTNEVLLVVE<GLRNQHSPIDGVEKYN<PKTQEWSF*ASITLKR---CS

Parental  VSLHDRIYVIGGYDGRSRLSSVECLDYTADEDGVWYSVAPMNVRRGLAGATTLGDMIYVSGGFDGSRRHT
          V.LHD.I.V.GGYDG.S..SSV.CLDY.ADE.GVWYSV.P.NV...L.G.TTLGD.I.V.GG.D.....T
Retrocopy VYLHDWICVMGGYDGHSHFSSVDCLDYPADEVGVWYSVTPRNVL*ALTGPTTLGDKICVPGGLDTTTYPT

Parental  SMERYDPNIDQWSMLGDMQTAREGAGLVVASGVIYCLGGYDG---LNILNSVEKYDPHTGHWTNVTPMAT
          ..ER.DPNIDQWS.LGDM.T..EG.G.VVASG.I.C.GGY.G...LNILNSV.KY.PHTG..TNVT.MAT
Retrocopy ITERWDPNIDQWSILGDM*TSWEGSGPVVASGLI-CQGGYYGYGGLNILNSVDKY-PHTGQ*TNVTQMAT

Parental  KRSGAGVALLNDHIYVMGGFDGTAHLSSVEAYNIRTDSWTTV-TSMTTPRCYVGATVLRGRLYAIA
          K.SGAG.ALLNDHIYV..G.DG..HLSSVEAYNI.TDSW......MTTP.CYVGA.VL.GR..AIA
Retrocopy KPSGAGGALLNDHIYV*RGLDGIGHLSSVEAYNIHTDSWKLA<ANMTTP*CYVGASVLQGRHCAIA

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_2103 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006231	1 retrocopy	retro_cjac_2151,
Dasypus novemcinctus	ENSDNOG00000010436	1 retrocopy	retro_dnov_2190,
Echinops telfairi	ENSETEG00000007800	2 retrocopies	retro_etel_2103 , retro_etel_723,
Homo sapiens	ENSG00000117153	1 retrocopy	retro_hsap_2545,
Macaca mulatta	ENSMMUG00000017849	1 retrocopy	retro_mmul_612,
Nomascus leucogenys	ENSNLEG00000018103	1 retrocopy	retro_nleu_2795,
Otolemur garnettii	ENSOGAG00000014771	1 retrocopy	retro_ogar_1552,
Pongo abelii	ENSPPYG00000000343	1 retrocopy	retro_pabe_1872,
Pan troglodytes	ENSPTRG00000001861	1 retrocopy	retro_ptro_1483,