RetrogeneDB ID: retro_etel_480

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_7929:67196..67914(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000007881
• Aliases: None
• Description: None

Sequence

>retro_etel_480
GGGCGTCCTGGCTACATCTGACAGCTTTCTGGCTTCCTTTCATGCAACTAGCTCACCACGCAGATCCTCAAGGAAGGCCT
GGCCACCTACCTGGACCAGGTGCGTGCCCTGGAGATGGCCAACACCAAACTGGAGGTGAAGATCTGCGACTGGTCCCCGA
AGCAGGGCCCACGGGGGCCCCACCTGGGACTACAGTCACTACTACAAGACCATTGAGGAGCTGCAGAGCAAGATGCTTGG
TGCCACCATCGAGAATGTCAAGATTGTGCTGCAGATTGACAATGCCCACCTGCCTGCAGATGACTTTCAGACTAAGTTAG
AGACGGAGCAGACCCTGTGTACAAGATTGGAGGCAGATATCCCTGGGCTGCACACGGAGCTGGATGAGCTGACCCTGCTT
AGCGTGGACCTGGGGATGCAGAGATGGAAGGGCTGAAGGGAAGGACTGGCCTCCCTGAATAAGAATCACAGGTTGGAAAT
CAGTGTTTTGAAGGCTCTGGTCAATGTGGAGGTGGATTCTGCACCCGGCATCGACCTGGCCAAGATTCAGAACGACATGA
AAAGCCAGTATGAGATCATGACTGAGAAGAACCGGAAGTATGCTGAAGCCTGGTTCATCAGCCAGACTGAGAACCTGAAC
TGGGAGGTTACTGGCCACAAAGAGCAGCTCCTGGTCAGCGAGATGGAGGTATCTGACCTGTGGTGGAGACTACAGTCT

Alignment

ORF - retro_etel_480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.86 %
• Parental protein coverage: 60.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GYGGVLSTSDGLLSGNEKITMQNLNDRLASYLDKVRALETANTDLEVKIRDWYQKQGP-GP-ARDYSHYY
          G..G......G.LS.N...T.Q.L...LA.YLD.VRALE.ANT.LEVKI.DW..KQGP.GP...DYSHYY
Retrocopy GRPGYI*QLSGFLSCN*-LTTQILKEGLATYLDQVRALEMANTKLEVKICDWSPKQGPRGP>TWDYSHYY

Parental  KTIEDLRDQILGATIQNSKVVLQIDNARLAADDFRTKFETEQALRVSVEADINGLRRVLDELTLARADLE
          KTIE.L....LGATI.N.K.VLQIDNA.L.ADDF.TK.ETEQ.L....EADI.GL...LDELTL...DL.
Retrocopy KTIEELQSKMLGATIENVKIVLQIDNAHLPADDFQTKLETEQTLCTRLEADIPGLHTELDELTLLSVDLG

Parental  MQ-IEGLKEELAFLKKNHEEEISVLKAQVGGQVSVEVDSTPGIDLAKILNDMRSQYELMAEKNRKDAEAW
          MQ...G..E.LA.L.KNH..EISVLKA.V.....VEVDS.PGIDLAKI.NDM.SQYE.M.EKNRK.AEAW
Retrocopy MQRWKG*REGLASLNKNHRLEISVLKALV----NVEVDSAPGIDLAKIQNDMKSQYEIMTEKNRKYAEAW

Parental  FIKQTEELKLEVDVHTEKLQVSKTEVTDLRRTLQS
          FI.QTE.L..EV..H.E.L.VS..EV.DL...LQS
Retrocopy FISQTENLNWEVTGHKEQLLVSEMEVSDLWWRLQS

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_480 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 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480 , retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337, retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697,