RetrogeneDB ID: retro_etel_633

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_10834:2975..3632(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000018599
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000012655
• Aliases: None
• Description: None

Sequence

>retro_etel_633
ATGTCACATCCTTCCCCCCCAAACTAAGCCCTCCAGCCCCAGCAACTCCCTAGTGCTCTTTGATGTGGACATCAGAGAGG
AGCAAGTTGGTCGAATTATCTTAGAGTCGTTTGCAAATACTGTGCCTAAAACTGCAGAAAACTTCCGTGTATTGTGTGTG
GGAGGGAAAGGCTTTGAACCCATAGCTGGAAAACCGCTCCATTTCAAAGAATAGTGCCCTTTCCGTGGGACTATTACAAG
ATTCATGATTCAGGGTGGCGACTTCTGAAATCAGAAGGGCACAGGGGGAGAAAGTATTTATGGTGAAAATTTTGAAGATG
AAAATTTCTATTATAAGCAGGAAGGTTTATTGACCATGGCAAATGCAGGACCAATACTAATGGTTCCCAGTTCTTTATCA
CAACTCTCCATTTGGATGGGAAGTGTGTGGTATTTGGCCAAGTCATTAAAGGACTGGGTGTGGCAAGGCTACTGGAAAAC
AAAGAAGTGGAAGGGGAAAACCTGCTACATGCTGCGCTGTTGCAGAATGCGGAGAATTGAACGAAGAGGGAGATTGGGGA
ATAGTCCCCAAAATGGCTCTGGTGACAGTCATCCGGATTTTCCTGTGAGTGCTGAGATAGATTTAAAGGGTGTAGTTAAG
TTTTATTGGTAACAGAC

Alignment

ORF - retro_etel_633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.61 %
• Parental protein coverage: 60.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSHPVP-QTKPSNPSNPRVFFDVDIGGEQVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHLK
          MSHP.P.QTKPS.PSN..V.FDVDI..EQVGRI.LE.FA..VPKTAENFR.LC.G.KG..P..GKPLH.K
Retrocopy MSHPSP>QTKPSSPSNSLVLFDVDIREEQVGRIILESFANTVPKTAENFRVLCVGGKGFEPIAGKPLHFK

Parental  G-CPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFYYKHDQEGLLSMANAGP-NTNGSQFFITTV
          ..CPF...I..FMIQGGDF.NQ.GTGGESIYGE.FEDENFYYK..QEGLL.MANAGP.NTNGSQFFITT.
Retrocopy E*CPFRGTITRFMIQGGDF*NQKGTGGESIYGENFEDENFYYK--QEGLLTMANAGP<NTNGSQFFITTL

Parental  PTPHLDGKHVVFGQVIKGMGVARMLENIEVEGE-KPAKLCIIAECGELKEGDDWGIFPK-DGSGDSYPDF
          ...HLDGK.VVFGQVIKG.GVAR.LEN.EVEGE.KPA..C..AECGEL.E..DWGI.PK..GSGDS.PDF
Retrocopy ---HLDGKCVVFGQVIKGLGVARLLENKEVEGE<KPATCCAVAECGELNEEGDWGIVPK<NGSGDSHPDF

Parental  PEDAEIDFKDVDK-ILLITE
          P..AEID.K.V.K..LL.T.
Retrocopy PVSAEIDLKGVVK<VLLVTD

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_633 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 16 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016680	1 retrocopy	retro_btau_1672,
Choloepus hoffmanni	ENSCHOG00000012069	1 retrocopy	retro_chof_1533,
Callithrix jacchus	ENSCJAG00000001437	2 retrocopies	retro_cjac_2321, retro_cjac_4162,
Cavia porcellus	ENSCPOG00000001046	2 retrocopies	retro_cpor_275, retro_cpor_436,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633 ,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Myotis lucifugus	ENSMLUG00000009317	1 retrocopy	retro_mluc_1667,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Mustela putorius furo	ENSMPUG00000018108	1 retrocopy	retro_mputfur_1415,
Mus musculus	ENSMUSG00000027804	6 retrocopies	retro_mmus_1086, retro_mmus_1888, retro_mmus_2228, retro_mmus_2555, retro_mmus_3254, retro_mmus_616,
Oryctolagus cuniculus	ENSOCUG00000006602	1 retrocopy	retro_ocun_1625,
Otolemur garnettii	ENSOGAG00000003317	2 retrocopies	retro_ogar_2355, retro_ogar_2680,
Pongo abelii	ENSPPYG00000015159	1 retrocopy	retro_pabe_3594,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,
Ictidomys tridecemlineatus	ENSSTOG00000001552	1 retrocopy	retro_itri_1422,
Tursiops truncatus	ENSTTRG00000016269	1 retrocopy	retro_ttru_1027,