RetrogeneDB ID: retro_etel_1695

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_288037:324..1094(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA4
• Ensembl ID: ENSETEG00000019546
• Aliases: None
• Description: karyopherin alpha 4 (importin alpha 3) [Source:HGNC Symbol;Acc:6397]

Sequence

>retro_etel_1695
TTGCACAATGATCGAATGCCCCCAATTGATGACCTAATAGAATCAGAATATTGCCTCTTTTTGTCCATTGTCTCGATGAG
ATTCCAACCCTTCTTTACAGTTTGAAGCTGCATGGACTTTGACAAACATTGTGTCTGGAACCTTTGACAAACGCAAGCAG
TCGTTCAATGCTGTACCACTCTTCCTAAGGCTTTTCCATTCCCCCCATCAAAATGCTTGCGAGCAAGCACGGACTGCTTT
GGGAGATGTTCTGGGTGATGGATTCTGGTGTAAGAGATTATGTCCTAAGCCTGGGAGTTGAGAAACCCTTACTTTCTTTC
ACAAGTCCTTCTATTCCTATAACATTCTTAAGAAACGTTGTTTGGGTTCGAGTCAATTTACGTAGCCACAAGGACGCACC
ATCCACAATGAGAACTATGTAAGAGATTCTCCCAGCTCTTTGTGTTTGAATTTATCAAGCAGATGCAAATAAATCGGTGG
AGACTGTCTGGGTCCTCTCTCACCCTACTGATGCTGGCAATGAACTGATGCAGATGGTCATAGATTCTGGAAGAGTTCCT
CATTTGGTTGCTCTGCTCAGCTACAGGAAGTGAAAGTTAAGACTGCTACACGTCAAGCTGCATGCAACATTGTTACTGTA
ACTGAGGAGCAGACACAAGTCAGTATCGGATTGAGATATGCTTTCACATCTTCCAGCACTTTGGACACATCCCAAAGAGA
AAATTACTAAAGAAGCAGTCTGGTTCCTCATAACCGCAGGACATCTACAA

Alignment

ORF - retro_etel_1695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.05 %
• Parental protein coverage: 52.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LSSDRNPPIDDLIKSG-ILPILVHCLER-DDNPS-QFEAAWALTNIASGTSEQTQAVVQSNAVPLFLRLL
          L..DR.PPIDDLI.S..ILP..VHCL...D.NPS.QFEAAW.LTNI.SGT..........NAVPLFLRL.
Retrocopy LHNDRMPPIDDLIESE<ILPLFVHCLDE<DSNPSLQFEAAWTLTNIVSGTFDKRKQ--SFNAVPLFLRLF

Parental  HSPHQNVCEQAVWALGNIIGDGPQC-RDYVISLGVVKPLLSFISPSIPITFLRNVTWVMVNLCRHKDPPP
          HSPHQN.CEQA..ALG...GDG..C.RDYV.SLGV.KPLLSF.SPSIPITFLRNV.WV.VNL..HKD.P.
Retrocopy HSPHQNACEQARTALGDVLGDGFWC>RDYVLSLGVEKPLLSFTSPSIPITFLRNVVWVRVNLRSHKDAPS

Parental  PMETIQEILPALCVLIHHTDVNILVDTVWALSYLTDAGNEQIQMVIDSGIVPHLVPLLSH-QEVKVQTAA
          .M.T..EILPALCV.I...D.N..V.TVW.LS..TDAGNE..QMVIDSG.VPHLV.LLS..QEVKV.TA.
Retrocopy TMRTM*EILPALCV*IYQADANKSVETVWVLSHPTDAGNELMQMVIDSGRVPHLVALLSY<QEVKVKTAT

Parental  LRAVGNIVTGTDEQTQV-VLNCDALSHFPALLTHPKEKINKEAVWFLSNITAGNQQ
          ..A..NIVT.T.EQTQV.V...D.LSH.PAL.THPKEKI.KEAVWFL..ITAG..Q
Retrocopy RQAACNIVTVTEEQTQV>VSD*DMLSHLPALWTHPKEKITKEAVWFL--ITAGHLQ

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_1695 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008565	2 retrocopies	retro_chof_1082, retro_chof_823,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Echinops telfairi	ENSETEG00000019546	1 retrocopy	retro_etel_1695 ,
Rattus norvegicus	ENSRNOG00000010768	1 retrocopy	retro_rnor_592,