RetrogeneDB ID: retro_etel_1583

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_280315:188..866(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000011253
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSETEG00000002717
• Aliases: None
• Description: None

Sequence

>retro_etel_1583
ACTGTCGAAAAGCACTCAGTGGAGTTATAAATGGCTTTTGAGTGCCTCACAATGAGGCTTAGATGAGGCGGCCGTTGTCA
TGCAATCTGCAAAGAACATGTATGAATTGCACAAGAAAAATCTCTCCAAATGAGCTCATCCTGGGCTGGTACACTACAGG
CCATGACATCACCGAGCTCTCTGTGCTGTTCCATTAGTACTACAACCCCATTCCCCTGCCTGTGGACACCAGCCTCCACA
AGAGCATCGAGGCCTCTGTCAGCACTTTAATGGGTATCTGTGGGAGGACATGATGCTGGTGTTTACACATCTGACCAGGA
AGTATGCATATTTACAACACAGAACACATCAGGGTTGACCTGATTGTGGAGCCCCATTTTAGCCTCCATGGGATGATCTG
CCTCTCAAGTGACTTGGAGCGAGTCAGAGGGGCATCAGTCCACATCCAGCAGGCCCTAAGCACACTGTTGCAGTATGCAG
AGGATGTACTGTCTGGAAAGGTATCAGCTGACAATACTGTGGGCAGTTTCTCGATAAGTCTGGTTAACCAAGTACCCAAA
CTCATGCCTCATGACTTTTGAGATCATGCTCAACAGCAACATCAATGGCCTGCTGATGGTAACCTACCTGGTTAATCTTA
TGTAGTCACAGATTGCCCTCAATGAGAAACTTGTCAAC

Alignment

ORF - retro_etel_1583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.33 %
• Parental protein coverage: 66.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  TVDKHSVE-VTNCFSVPHNES-EDEVAVDMEFAKNMYELHKK-VSPNELILGWYATGHDITEHSVLIHEY
          TV.KHSVE.V.N.F.VPHNE...DE.AV.M..AKNMYELHKK..SPNELILGWY.TGHDITE.SVL.H.Y
Retrocopy TVEKHSVE<VINGF*VPHNEA<LDEAAVVMQSAKNMYELHKK>ISPNELILGWYTTGHDITELSVLFH*Y

Parental  YSREAPNPIHLTVDTSLQNGRMSIKAYMSTLMGVPGRT-MGVMFTPLTVRYAY-YDTERIGVDLIMKTCF
          Y....P.P....VDTSL.....SI.A..STLMG..GRT.M...FT.LT..YAY.Y.TE.I.VDLI....F
Retrocopy YN---PIPL--PVDTSLHK---SIEASVSTLMGICGRT<MMLVFTHLTRKYAY>YNTEHIRVDLIVEPHF

Parental  SSNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPDD-FETM
          S....I.LSSDL..V.GAS..IQ.ALST.LQYAEDVLSGKVSADNTVG.F..SLVNQVPK..P.D.FE.M
Retrocopy SLHGMICLSSDLERVRGASVHIQQALSTLLQYAEDVLSGKVSADNTVGSFSISLVNQVPKLMPHD>FEIM

Parental  LNSNINDLLMVTYLANLTQSQIALNEKLVN
          LNSNIN.LLMVTYL.NL..SQIALNEKLVN
Retrocopy LNSNINGLLMVTYLVNLM*SQIALNEKLVN

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_1583 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 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Canis familiaris	ENSCAFG00000006884	1 retrocopy	retro_cfam_1339,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Erinaceus europaeus	ENSEEUG00000001226	1 retrocopy	retro_eeur_130,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583 , retro_etel_35,
Homo sapiens	ENSG00000175390	3 retrocopies	retro_hsap_2106, retro_hsap_2512, retro_hsap_4321,
Gorilla gorilla	ENSGGOG00000011702	5 retrocopies	retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589, retro_ggor_1590,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Macaca mulatta	ENSMMUG00000015010	1 retrocopy	retro_mmul_412,
Oryctolagus cuniculus	ENSOCUG00000004225	1 retrocopy	retro_ocun_1488,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175,
Pan troglodytes	ENSPTRG00000003326	1 retrocopy	retro_ptro_197,
Pteropus vampyrus	ENSPVAG00000015764	1 retrocopy	retro_pvam_371,