RetrogeneDB ID: retro_etel_837

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_172987:3201..3842(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11A
• Ensembl ID: ENSETEG00000004920
• Aliases: None
• Description: RAB11A, member RAS oncogene family [Source:HGNC Symbol;Acc:9760]

Sequence

>retro_etel_837
ATGGGCACCCGCAAAAAGGAGTACAACTACCTCTTCAAAGGTGTCTTTATTGGAGTTTCTGGTGTTGGAAAGAGTAATCT
CCTGTCTCGATTCACTCGAAAATGAGTTTAATCTGGAGAGCAAGAGCACCATTGGAGTAGAGTTTGCAACAAGAAGCATT
CAGGTGGATGGAAAAACAATGAAGACACAGGTATGGGACACAGCGGGGCAAGAGCGATACCGAGCGATAACATCAGCATG
CTGTCATGGAGCTGTAGGTGCCTTATAGGTTTATGACATTGCTGAACATCTCACATATGAAAATGCTGAACGGTGGCTGA
AAGAATTGAGGGGTCACGCTGATAGTAACATTGTGAACATGCTTGTGGGAAATAAGAGTGATTTACGCCATCTCAGGGCA
GTCCCTGCAGATGAAGCAAGAGCTCTTGCAGAAAAGAATGGTTTGTCATTCATTTGAGACTTCTGCTCTAGACTCAACAA
ATGTAGAAGCTGCTTTTCAAACAATCCTGACAGAGATATACCGCATTGTTTCTCAGAAGCAATTGTCAGACAGACGTGAA
AATGACATGTCTCCAAGCAACAATGTGGTCCCTATTCATGTTCCACCAACCACTGACAACAAGCCAAAGGTGCAGTGTTG
C

Alignment

ORF - retro_etel_837 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.12 %
• Parental protein coverage: 98.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTR-NEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAG
          MGTR..EY.YLFK.V.IG.SGVGKSNLLSRFTR.NEFNLESKSTIGVEFATRSIQVDGKT.K.Q.WDTAG
Retrocopy MGTRKKEYNYLFKGVFIGVSGVGKSNLLSRFTR>NEFNLESKSTIGVEFATRSIQVDGKTMKTQVWDTAG

Parental  QERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTDEA
          QERYRAITSA...GAVGAL.VYDIA.HLTYEN.ERWLKELR.HADSNIV.MLVGNKSDLRHLRAVP.DEA
Retrocopy QERYRAITSACCHGAVGAL*VYDIAEHLTYENAERWLKELRGHADSNIVNMLVGNKSDLRHLRAVPADEA

Parental  RAFAEKNGLSFI-ETSALDSTNVEAAFQTILTEIHHTVSQKQVPNRHENDMSPRNTGVPIHVPPTTDNKP
          RA.AEKNGLSFI.ETSALDSTNVEAAFQTILTEI...VSQKQ...R.ENDMSP.N..VPIHVPPTTDNKP
Retrocopy RALAEKNGLSFI>ETSALDSTNVEAAFQTILTEIYRIVSQKQLSDRRENDMSPSNNVVPIHVPPTTDNKP

Parental  NVQCC
          .VQCC
Retrocopy KVQCC

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_837 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 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018959	1 retrocopy	retro_btau_1850,
Callithrix jacchus	ENSCJAG00000007333	1 retrocopy	retro_cjac_1050,
Echinops telfairi	ENSETEG00000004920	5 retrocopies	retro_etel_1150, retro_etel_2132, retro_etel_2214, retro_etel_694, retro_etel_837 ,
Echinops telfairi	ENSETEG00000010340	2 retrocopies	retro_etel_203, retro_etel_32,
Echinops telfairi	ENSETEG00000018042	3 retrocopies	retro_etel_1163, retro_etel_122, retro_etel_681,
Homo sapiens	ENSG00000103769	1 retrocopy	retro_hsap_715,
Gorilla gorilla	ENSGGOG00000014252	2 retrocopies	retro_ggor_538, retro_ggor_605,
Myotis lucifugus	ENSMLUG00000008820	2 retrocopies	retro_mluc_1606, retro_mluc_2435,
Macaca mulatta	ENSMMUG00000008006	1 retrocopy	retro_mmul_2463,
Nomascus leucogenys	ENSNLEG00000012853	1 retrocopy	retro_nleu_467,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pongo abelii	ENSPPYG00000006573	1 retrocopy	retro_pabe_618,
Pan troglodytes	ENSPTRG00000007188	1 retrocopy	retro_ptro_510,