RetrogeneDB ID: retro_etel_1685

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_287423:32587..33286(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000019556
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000001809
• Aliases: None
• Description: None

Sequence

>retro_etel_1685
GGGGTTCAACATGTACTAGAATGTTTCATTCTGGCTGGGGATTAGGTGGTCCTCGTGCTCATAAATCAAAGATACCCTTT
ACTATCGGTTTTACTGATGGATCTTCTTCTTCTCAGAGTTCATAGTCTCCAAGAGTAGGGAAGCCGTGGATCCTATAGCT
GAGCTTTTACCTCACTTACCAGGAGTGAAATGCTCTGCAGGAGGACAACGTAATTATTCGGGCCCTTCTGCTTCTCAGTC
CCAACAAAGAGCAGCAGCTTCACTCGAGCAGCAGCATGCCCAGACAGCAAGGGAGCAACTGAAGGCCACACACGTCACAA
CCTGGCATACTAACACAAGCAGTGTCACCACCACAATCACACAATCCACAGCAACCACCAGCACAGCGAATTCAGAAAGC
AGTCAGCAAGCGATCCAGAATTCCCAGTTTCATTTAACCAGGTTGAATGATCCTAAGACGTCTGAAGCCGAGCGCCCGTC
CTCGGAAAGTGAGTGTACAGACGGCAGCCTGTTTGTCCACGAGCTCCTTCAGTCGGCTTCAGGACGTGAAGAAAGCTCGT
CGTCAGTTGAGGATAAACGCCGGGAGAGGTCAGATTTTGGTGCTATGGGCTGTGTAGCTATTATGCCTTTAGATGTTGCT
TTAGAAAACCTAAATTGAAAGAGAGTAAGAAGGGAAATGAGCCTCCACCACCTCCACTT

Alignment

ORF - retro_etel_1685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.17 %
• Parental protein coverage: 61.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GVRHV-RRMFHPGRGLGGPRARRSNMHFTSSSTGGLASSQSSYSP-SNREAMDPIAELLSQLSGVRRSAG
          GV.HV..RMFH.G.GLGGPRA..S...FT...T.G..SSQSS.SP...REA.DPIAELL..L.GV..SAG
Retrocopy GVQHV<TRMFHSGWGLGGPRAHKSKIPFTIGFTDGSSSSQSS*SP<KSREAVDPIAELLPHLPGVKCSAG

Parental  GQLNSSGPSASQLQQLQMQLQLERQHAQAARQQLETARNATRRTNTSSVTTTITQSTATTNTATTESSQQ
          GQ.N.SGPSASQ.QQ......LE.QHAQ.AR.QL......T..TNTSSVTTTITQSTATT.TA..ESSQQ
Retrocopy GQRNYSGPSASQSQQ-RAAASLEQQHAQTAREQLKATHVTTWHTNTSSVTTTITQSTATTSTANSESSQQ

Parental  AIQNSQFLLTRLNDPKMSETERQSMESERADRSLFVQELLLSTLVREESSSSDEDDRGEMADFGAMGCVD
          AIQNSQF.LTRLNDPK.SE.ER.S.ESE..D.SLFV.ELL.S...REESSSS.ED.R.E..DFGAMGCV.
Retrocopy AIQNSQFHLTRLNDPKTSEAERPSSESECTDGSLFVHELLQSASGREESSSSVEDKRRERSDFGAMGCVA

Parental  IMPLDVALENLN-LRESNKGNEPPPPPL
          IMPLDVALENLN.L.ES.KGNEPPPPPL
Retrocopy IMPLDVALENLN<LKESKKGNEPPPPPL

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_1685 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005786	1 retrocopy	retro_chof_1282,
Dasypus novemcinctus	ENSDNOG00000006752	2 retrocopies	retro_dnov_1000, retro_dnov_2063,
Echinops telfairi	ENSETEG00000001809	1 retrocopy	retro_etel_1685 ,
Myotis lucifugus	ENSMLUG00000000979	1 retrocopy	retro_mluc_1781,
Monodelphis domestica	ENSMODG00000015567	1 retrocopy	retro_mdom_1682,
Otolemur garnettii	ENSOGAG00000034863	2 retrocopies	retro_ogar_3140, retro_ogar_397,
Vicugna pacos	ENSVPAG00000010386	1 retrocopy	retro_vpac_650,