RetrogeneDB ID: retro_etel_1993

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_322363:41869..42690(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000006918
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TUBA4A
• Ensembl ID: ENSETEG00000010296
• Aliases: None
• Description: tubulin, alpha 4a [Source:HGNC Symbol;Acc:12407]

Sequence

>retro_etel_1993
ATGAATCTCAGTCCACGTGGTGTCCAGAGGGGCAACGCCTGCGGCAGCTCTACTGCCTGGATCACGGGATTCAGCCTGAT
GGGCAGATGCCCAGCGACAAGACCGTTGGTGGGAGAGACGACTCCTTCACCACCTTCTTCTGTGAAACTGGGGTTGGGAA
GCCCGTGTCCCGGGCCGTGTTTGTGGACCTGGCGCCCACGGTGATCGATGAGACCCGAAAGGGCCCGTACCACCAGCTGT
TCCATCCAGAGCAGCTTGTCACCGGCAAGGAGGATGCTGCAAACAACGACGCCTGAGGCCACTCTGCCTTCGGCCAGGAG
ATCCTCAACCCGGTGCTGGACCGCCTCCGCAAGCTGTTGGACCAGCGCACGGGACTCCAGGCTGCCTGGTCCGGCACAGC
TTTGGCAGCGGCCAGGGCTCGGGCTTCACCTAGCCGCTGATGGAGCGGCCCTCGGCGGACTATGGAAAGAAGTCCACGCT
GGAGTTGCCCATCTCCCCAGCCCTCTAGCCTTCGCGGCCATGGTCGAGCCCTACAACCCCATCCTGACCACCCACACCAC
CCTGGAGCCCTCCGACTACGCCTTCATGGGGGACAACGAGGCCATCAGCGACAGCTGCCGCTGCAACCTGAACCTCGAGC
GCCCAACCGACACCAGCCTCAAACGCCTCCTCGGCCCAATCCTGTCCTCCATCGCGGCTTCCCTGCGCTTCAACAGAGCC
CTCCATGTGGACCTGACCAAGTTCCAGATCAACCTGGCACCTTCCCCTCGCATCCACTCCCCAGGGCCACCTATGCACAC
CTCATCTCTGCCGAGAAGGCC

Alignment

ORF - retro_etel_1993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.61 %
• Parental protein coverage: 61.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VHVGQAGVQMGNACW-ELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDLEPTVI
          ......GVQ.GNAC...LYCL.HGIQPDGQMPSDKT.GG.DDSFTTFFCETG.GK.V.RAVFVDL.PTVI
Retrocopy MNLSPRGVQRGNACG<QLYCLDHGIQPDGQMPSDKTVGGRDDSFTTFFCETGVGKPVSRAVFVDLAPTVI

Parental  DEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGLQ-GFLVFHSFGGG
          DE.R.GPY.QLFHPEQL.TGKEDAANN.A.GH...G.EI..PVLDR.RKL.DQ.TGLQ.G.LV.HSFG.G
Retrocopy DETRKGPYHQLFHPEQLVTGKEDAANNDA*GHSAFGQEILNPVLDRLRKLLDQRTGLQ<GCLVRHSFGSG

Parental  TGSGFTSLLMERLSVDYGKKSKLEFSIYPA-PQVSTAVVEPYNSILTNHTTLEHSDCAFMVDNEAIYDIG
          .GSGFT..LMER.S.DYGKKS.LE..I.PA.P....A.VEPYN.ILT.HTTLE.SD.AFM.DNEAI.D..
Retrocopy QGSGFT*PLMERPSADYGKKSTLELPISPA<PLAFAAMVEPYNPILTTHTTLEPSDYAFMGDNEAISDSC

Parental  RSNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIH-FPLATYAPVISAEKA
          R.NL..ERPT.T.L.RL...I.SSI.ASLRF..AL.VDLT.FQ.NL.P.PRIH..P.ATYA..ISAEKA
Retrocopy RCNLNLERPTDTSLKRLLGPILSSIAASLRFNRALHVDLTKFQINLAPSPRIH<LPRATYAHLISAEKA

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_1993 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Dipodomys ordii	ENSDORG00000000154	3 retrocopies	retro_dord_460, retro_dord_564, retro_dord_786,
Echinops telfairi	ENSETEG00000010296	2 retrocopies	retro_etel_1816, retro_etel_1993 ,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Microcebus murinus	ENSMICG00000000804	1 retrocopy	retro_mmur_103,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000010798	1 retrocopy	retro_pvam_1019,
Rattus norvegicus	ENSRNOG00000003597	1 retrocopy	retro_rnor_2819,
Ictidomys tridecemlineatus	ENSSTOG00000019497	1 retrocopy	retro_itri_203,
Tursiops truncatus	ENSTTRG00000010042	1 retrocopy	retro_ttru_531,