RetrogeneDB ID: retro_etel_1816

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_301670:2715..3938(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000007539
• 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_1816
ATGTACAAGCACATCTCAGTCCATGTGGGCCAGGCTGGTGTGCAGATTGGCAACGCCGGCTGGGAGCTCTACTGCTTGGA
GCATGGGATCCAACCCGATGGGCAGAAGTCCTGTGACAAGGCCAGTGGGGGAGGGGATGACTCCTTCAAAACCTTCTTCA
GTGAAACTGGGGCAGGGAAGCACATGCCCCAGGTGGTGTTTGTGGACCTGGAGCCCATGGTGATCGATGAGGTTCGGACT
GACACATACCGCCAGCTCTTCCATCCAGAGCAGCTCATCACAGGCAAGGAAGATGCCACCAATAACTATGCCCGGGGACA
CTACACCACTGGAAAGGAGCTCATTGACCTGGTGCTGGACCGGATTCGGAAGCTGTCTGACCAGTGCACAGGGCTCCAGG
ACTTCCTCATCTTCCACAGCTTTGGCGGAGGTACGGGCTTCACCTCCCTGCAGATGGAGCGGCTCTCGGTGGACTACAGC
AAGAAGTCCAACCTGGACTTCTCCATCTACCCAGCTCCCCACATCTCCACGGCCGTGGTCGAGTCCTACAACTCCATCCT
GACCACCCACGCCACCCTGGAGCACTCTGACTGCACCTTCATGGTGGACAATGAGACCATCTATTGACATCTGTCACCGC
AACCTGGATATTGAGTGCCTGACCTACACTCACCTCAACTGCCTCATAGGCCAAATCGTGTACTCCATCACGGCTTCCCT
GTGCTTCGACGGTGCCCTCAATGTGGACCTGACCGAGTTCCAGACCAACCTAGTGTCCTACCCTCGCATCCACTTCCCCT
GGCCACCTATGCGCCTGTCATCTCTGCCGAGAAGGCCTACCATGAACAGCTGTCCGTGGCCAAGATCACCAACGTCTGCT
TTGAGCCTGCCAACCAGATGATGAAGTGCGACCCCCACCACGGCAAGTACATGGCCTGCTGCCTGCTGTACCGTGGAGCC
ATGGTGCCCAAGGATGCCAATGCTGCCATCGCCACCATCAAGACCAAGCGTACTATCCAGTTTGTGGACTGGTGCCCAAT
GGGCTTCAAGGTTGGCATCAACTACCAGCCACCCACTGTGGTGTCCGGGGTGACCTGGCGAAGGTGCAGTGTGTCATGTG
CATGCTGAGCAACATGACCTCCATCGCCGAGGCCTGGGCGCGCCTGGACCACAAGTTTGACCTGATGTATGCCAAGCGGG
GGTTCATGCACTGGTATGTGGGC

Alignment

ORF - retro_etel_1816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.57 %
• Parental protein coverage: 91.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDL
          M...ISVHVGQAGVQ.GNA.WELYCLEHGIQPDGQ...DK..GGGDDSF.TFF.ETGAGKH.P..VFVDL
Retrocopy MYKHISVHVGQAGVQIGNAGWELYCLEHGIQPDGQKSCDKASGGGDDSFKTFFSETGAGKHMPQVVFVDL

Parental  EPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGLQGFLVFHS
          EP.VIDE.R...YRQLFHPEQLITGKEDA.NNYARGHYT.GKE.ID.VLDRIRKLSDQCTGLQ.FL.FHS
Retrocopy EPMVIDEVRTDTYRQLFHPEQLITGKEDATNNYARGHYTTGKELIDLVLDRIRKLSDQCTGLQDFLIFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTNHTTLEHSDCAFMVDNEAIY
          FGGGT..GFTSL.MERLSVDY.KKS.L.FSIYPAP..STAVVE.YNSILT.H.TLEHSDC.FMVDNE.IY
Retrocopy FGGGT--GFTSLQMERLSVDYSKKSNLDFSIYPAPHISTAVVESYNSILTTHATLEHSDCTFMVDNETIY

Parental  -DIGRSNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHF-PLATYAPVISA
          .DI...NLDIE..TYT.LN.LI.QIV.SITASL.FDGALNVDLTEFQTNLV.YPRIHF.PLATYAPVISA
Retrocopy >DICHRNLDIECLTYTHLNCLIGQIVYSITASLCFDGALNVDLTEFQTNLVSYPRIHF<PLATYAPVISA

Parental  EKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIAAIKTKRSIQFVDWCP
          EKAYHEQLSVA.ITN.CFEPANQM.KCDP.HGKYMACCLLYRG..VPKD.NAAIA.IKTKR.IQFVDWCP
Retrocopy EKAYHEQLSVAKITNVCFEPANQMMKCDPHHGKYMACCLLYRGAMVPKDANAAIATIKTKRTIQFVDWCP

Parental  TGFKVGINYQPPTVVPG-GDLAKVQRAVCMLSNTTAIAEAWERLDHKFDLMYAKRPFVHWYVG
          .GFKVGINYQPPTVV.G.GDLAKVQ...CMLSN.T.IAEAW.RLDHKFDLMYAKR.F.HWYVG
Retrocopy MGFKVGINYQPPTVVSG<GDLAKVQCVMCMLSNMTSIAEAWARLDHKFDLMYAKRGFMHWYVG

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_1816 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 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,