RetrogeneDB ID: retro_etel_1478

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_272486:1917..2873(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT7
• Ensembl ID: ENSETEG00000009409
• Aliases: None
• Description: chaperonin containing TCP1, subunit 7 (eta) [Source:HGNC Symbol;Acc:1622]

Sequence

>retro_etel_1478
AAGACATTCTCTTACGCTGGGTTTGAAATGCAACCCAAAAAGTACAGTAACCCCAAGATTGCCCTGCTGAACGTGGAGCT
GGAACTGAAAGCCGAGAAGGACAACGCTGAGGTCCGAGTGCACACAGTGGAGGATTATCAGGCAATTGTTGATGCGGAGT
GGAACATTCTCTATGACAAGCTGGAGAAGATCCATCGTTCTGGAGCCAACGTCGTCTTGTCCAAACTCCCTATTGGGGAT
GTGGCCACCCAGTACTTTGCTGACCGGGACATGTTCTGTGCTGGCCGAATGCCCGAAGAGGATCTGAAGAGGACAATGAT
GACCTGCGGAGGCTCCATCCAGACCAGTGTGGACTCTCTGTCTGCAGAAGTGCTGGCAGCTGCCAGGTCTTCGAGGAGAC
CCAGATTGGATGCGAGAGGTACAGTTTCTTCACGGGCTGCCCGAAGGCCAAGACCTGCACGATCATCCTCCGCGGCGGTG
CCGAGCAGTTTATGGAGGAGACAGAGCGGTCCCTGCATGACGCCATCATGATTGTCACGCGCGCCATCAAGAACGATTCG
GTGGTGGCTGGCGGTGGGGCCATTGAGATGGAGCTCTCCAAGTACCTTCGGGATTACTAAAGGACCATCCCCGGGAAGCA
GCAGCTGCTGATCGGGGCCTATGCCAAGGCCTTGGAGATCATCCCACGCCAGCTGTGCAACAACGCGGGCTTCGATGCCA
CAAACATCCTCAACAAGCTGCGCCCCGCGTGGCATGCCCAGGGAGGCATGTGGTACGGGGTGGACATCAACAACAAGGAC
ATTGCTGACACTTTCGAGGCCTTCGTGTGGGAGCCAGCGATGGTGCGCGTCAATGCCCTGACGGCAGCCTCAGAGGCCGC
CCGTGCCATCGTGTCTGTAGATGAAACCATCAAGAACCCTCGCTCCATTGTGGACGCTCCACCACCGGGGCCGAGG

Alignment

ORF - retro_etel_1478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.25 %
• Parental protein coverage: 58.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTFSYAGFEMQPKKYSNPKIALLNVELELKAEKDNAEVRVHTVEDYQAIVDAEWDILYDKLEKIHRSGAK
          KTFSYAGFEMQPKKYSNPKIALLNVELELKAEKDNAEVRVHTVEDYQAIVDAEW.ILYDKLEKIHRSGA.
Retrocopy KTFSYAGFEMQPKKYSNPKIALLNVELELKAEKDNAEVRVHTVEDYQAIVDAEWNILYDKLEKIHRSGAN

Parental  VVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMM-CGGSIQTSVNALSAEVL-GSCQGFEETQIGSE
          VVLSKLPIGDVATQYFADRDMFCAGR.PEEDLKRTMM.CGGSIQTSV..LSAEVL.GSCQ.FEETQIG.E
Retrocopy VVLSKLPIGDVATQYFADRDMFCAGRMPEEDLKRTMMTCGGSIQTSVDSLSAEVL<GSCQVFEETQIGCE

Parental  RYNFFTGCPKAKTCTIILRGGAVQFMEETERSLHDAIMIVRRAIKNDSGVAGGGAIEMELSKYLRDYSRT
          RY.FFTGCPKAKTCTIILRGGA.QFMEETERSLHDAIMIV.RAIKNDS.VAGGGAIEMELSKYLRDY.RT
Retrocopy RYSFFTGCPKAKTCTIILRGGAEQFMEETERSLHDAIMIVTRAIKNDSVVAGGGAIEMELSKYLRDY*RT

Parental  IPGKQQLLIRAYAKALEIIPRQLCDNTGFDATNILNKL--ARHAQEGMWYGVDINNEDIADNFEAFVWEP
          IPGKQQLLI.AYAKALEIIPRQLC.N.GFDATNILNKL..A.HAQ.GMWYGVDINN.DIAD.FEAFVWEP
Retrocopy IPGKQQLLIGAYAKALEIIPRQLCNNAGFDATNILNKLRPAWHAQGGMWYGVDINNKDIADTFEAFVWEP

Parental  AMVRVNALTAASEAVCLIVSVDETIKNPRSTVDAPPPGVR
          AMVRVNALTAASEA...IVSVDETIKNPRS.VDAPPPG.R
Retrocopy AMVRVNALTAASEAARAIVSVDETIKNPRSIVDAPPPGPR

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_1478 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008879	1 retrocopy	retro_cfam_151,
Choloepus hoffmanni	ENSCHOG00000007937	1 retrocopy	retro_chof_2313,
Echinops telfairi	ENSETEG00000009409	2 retrocopies	retro_etel_1478 , retro_etel_607,
Gorilla gorilla	ENSGGOG00000007766	1 retrocopy	retro_ggor_2274,
Macropus eugenii	ENSMEUG00000000416	1 retrocopy	retro_meug_1995,
Macaca mulatta	ENSMMUG00000012448	1 retrocopy	retro_mmul_2093,
Otolemur garnettii	ENSOGAG00000009162	2 retrocopies	retro_ogar_2001, retro_ogar_2698,
Tupaia belangeri	ENSTBEG00000002066	2 retrocopies	retro_tbel_3708, retro_tbel_3751,