RetrogeneDB ID: retro_etel_2000

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_323612:48351..49485(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000019521
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GK
• Ensembl ID: ENSETEG00000008279
• Aliases: None
• Description: glycerol kinase [Source:HGNC Symbol;Acc:4289]

Sequence

>retro_etel_2000
ATGGCAGCCCCGAAGGAAGCGGTGGAGGGGCCATTGGTGGGGGCGGTGGTCCAAAGCACTAGTCACAGTCGCTTTCTTGT
TTTCAATGCGAAAACAGCAGGAATACTTACTCATTATCGAGTGGAACTAACGCAAGAGTTCCCAAAAGAAGGATGGGTGG
AACAAGACCCTAAGGAAATCCTCCAGTCTGTCTATGAATGCATAGAAAAAACATGCGAGAAACTCGATGAACTAAACATA
GCTCTATCCAACATAAAAGCTATCGGAATCAGCAACCAGAGGGAGACCGCGATCGTCTGGGACAAGTTAACCGGAGAGCC
TCTCTACAATGCTGTGGTGTGGCTGGATCTTCGAAGTCAGAGCACCGTCGAGAATCTCGGTAAAAAGATACCTGGGAATA
ACAACTTTGTCAAGTCGAAGACTGGCCTGCCACTGAGCACTTACTTCAGTGCCGTGAAACTTCGCTGGATGCTTGACAAC
GTGAGACAAGTTTCAAAAGGCGGTTGAAGAAGGGGAGAGCTCTTTTCGGCACCATCGATTCGTGGCTCATCTGGAGTTTG
ACAGGCGGAGTCAACGGGGGTGTCCATTGCACAGACGTAACAAATGCAAGTAGGACGATGCTTTTTCAACATTCATTCTT
TGGAGTGGGATAAAGAACTTTGTGACTTTTTTGAAATTCCGATGGACATTCTCCCCAAAGTTTGGAGTTGTTCAGAGATA
TATGGCGAAATGAAAACTGGGTCGTTGGTAGGTGTGCCGATATCTGGATGCTTAGGGGACCAATCTGCCGCATTAATAGG
ACAAATGTGCTTTGAAGAAGGACAGGCCAAAAACACATATGGAACAGACTGTTTCTTACTATGTAATACGGGTCGAAAGT
GTGTGTTTTCTGAGCATGGTCTTCTGACCACGGTAGCTTACAAACTTGGCAAAGACAAGCCAGTTATTTACGCACTGGAA
GGGTCTGTGGCTATAGCCGGTGCTGTTGTTCGTTGGCTAAAAGACAATCTTGGGATCCTAAGTAGCCCAGAAGAAATAGA
AGTACTTGCCAAAGAAGTAGGTACTTCTTACGGCTGTTACTTCATCCCAGCATTTTCAGGATTATATGCACCGTATTGGC
CCCCCCAGTGCCAG

Alignment

ORF - retro_etel_2000 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.42 %
• Parental protein coverage: 68.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAARKAALGPLVGAVDQGTSSTRFLVFNSRTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
          MAA...A..GPLVGAV.Q.TS..RFLVFN..TA..L.H..VE..QEFP.EGWVEQDPKEILQSVYECIEK
Retrocopy MAAPKEAVEGPLVGAVVQSTSHSRFLVFNAKTAGILTHYRVELTQEFPKEGWVEQDPKEILQSVYECIEK

Parental  TCEKLRELNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNN-FVKSK
          TCEKL.ELNI..SNIKAIG.SNQRET..VWDKLTGEPLYNAVVWLDLR.QSTVENL.K.IPGNN.FVKSK
Retrocopy TCEKLDELNIALSNIKAIGISNQRETAIVWDKLTGEPLYNAVVWLDLRSQSTVENLGKKIPGNNNFVKSK

Parental  TGLPLSTYFSAVKLRWILDNVRKV-QKAVEEN-RALFGTIDSWLIWSLTGGAKGGVHCTDVTNASRTML-
          TGLPLSTYFSAVKLRW.LDNVR.V.QKAVEE..RALFGTIDSWLIWSLTGG..GGVHCTDVTNASRTML.
Retrocopy TGLPLSTYFSAVKLRWMLDNVRQV>QKAVEEG>RALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTML>

Parental  FNIHSLEWDKELCDFFEIPMAILPSVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKN
          FNIHSLEWDKELCDFFEIPM.ILP.V.S.SEIYG.MK.G.L.GVPISGCLGDQSAAL.GQMCF..GQAKN
Retrocopy FNIHSLEWDKELCDFFEIPMDILPKVWSCSEIYGEMKTGSLVGVPISGCLGDQSAALIGQMCFEEGQAKN

Parental  TYGTGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIISTSEEIEK
          TYGT.CFLLCNTG.KCVFSEHGLLTTVAYKLG.DKPV.YALEGSVAIAGAV.RWL.DNLGI.S..EEIE.
Retrocopy TYGTDCFLLCNTGRKCVFSEHGLLTTVAYKLGKDKPVIYALEGSVAIAGAVVRWLKDNLGILSSPEEIEV

Parental  LAKEVGTSYGCYFVPAFSGLYAPYWEPSAR
          LAKEVGTSYGCYF.PAFSGLYAPYW.P...
Retrocopy LAKEVGTSYGCYFIPAFSGLYAPYWPPQCQ

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_2000 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 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007633	3 retrocopies	retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Echinops telfairi	ENSETEG00000008279	2 retrocopies	retro_etel_2000 , retro_etel_247,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Homo sapiens	ENSG00000198814	4 retrocopies	retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana	ENSLAFG00000007632	1 retrocopy	retro_lafr_30,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Mus musculus	ENSMUSG00000025059	2 retrocopies	retro_mmus_119, retro_mmus_97,
Nomascus leucogenys	ENSNLEG00000010102	2 retrocopies	retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Rattus norvegicus	ENSRNOG00000034116	2 retrocopies	retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,
Ictidomys tridecemlineatus	ENSSTOG00000008732	1 retrocopy	retro_itri_1436,
Tarsius syrichta	ENSTSYG00000008249	1 retrocopy	retro_tsyr_29,