RetrogeneDB ID: retro_eeur_669

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_379115:8205..9537(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1C
• Ensembl ID: ENSEEUG00000004068
• Aliases: None
• Description: tubulin, alpha 1c [Source:HGNC Symbol;Acc:20768]

Sequence

>retro_eeur_669
GAGTGCATCTCCATCCATGTTGGCCAGGCTGGTGTCCAGATCGGCAATGCCTGCTGGGAGCTCTACTGCCTGGAGCACGG
CATCCAGCCTGATGGCCAGATGCCCAGTGACAAGTTTACTGGGAATGGAGATGACTCCTTCAACACCTTCTTCAGTGAGA
CAGGTGCTGGCAAGCTTGTGCCCAGGGCAGTGTTTGTAGACCTGCAACCCATAGTCATTGATGAAATTCACAAAGGCCCC
TACCGACAGCTCTTCCACCCTGATAATTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGTCTGTGGGCACTACACC
TTGGGCAGGGAGATTATAGACCATGTCTCAGATCGAATTCGGACAGTGGCCCACCAGTGCACAGGTCTTCAGGACTTCCT
GGTTTTCCATAGCTTTGGTGGGGGAGCTGGCTTTGGGTTCACCTTTCTGCTGATGGAGTGTCTCTGTGTCGACTACGGCA
GAAAGTTCAAGCTCGAGTTCTCTATCTGCCCAGCCTCCCGGTCTCCACAGCTGTAGTGAAGCCCTACAGCTCCATCCTTA
CCACTCACAGCACCCTGGAGCATTGTGACTGTGCCTTCATGGTTGACAATGAAGCCATCTATGACATCTGTTGAAGGAAT
CTGGATATTGAACGACCAACTTACATTAACCTCAATCACCTTATTAGTCAGGTAGTGTCCTCCATCACTGCTTCCCTCAG
GTTTGATGGAGCCCTGAATGTTGACCTGGCAGAACTCCAGACCAACTTGGTGCCCTACCCCCACATCCACTTCCCTTTAA
CCACCTACGCCCTTGCCATCTCTGCTGAGAAAGCCTATCATCAACAGTTTTCTGTTCTAGAGTTCACCAATGTGTGTTTT
GAGTCAGCCAACCAGATGGTGAAATGTGACCCTCGCTATGGTAAATACATGGCCTGCTGCCTGTTGCACCATGGTGATGT
GGTCCCCAAAGATGTCAGTGCTGCCATTGCCAGCATCAAGACCAAGCATAGCATCCAGTTTGTGGACTGGTACCCTGCTG
GCTTCAAAGTTGACATTAATTACCAGCCTCCTACTGTGGTCCCTGGTGGAGACCTGGCCAAGGTCGAGTGGGCTGTGTGC
ATGCTGAGCAAGACCACGGTCATTGCTGAGGCCTGGGCCCGACTGAAGCACAAATTTGACCTGCTGTTTGCCAAGTGTGC
CTTTGTTCATTGGTATGTGGGTGAGGGCATAGGGGAGGGAGAGTTTTCTGAGGCCCGTGAGGACATGGCTACCCTAGAGA
AGGATTATGAGGAGTAGGAGCAGATAGTGCCGCTGGAGATGAGAATCCAGAG

Alignment

ORF - retro_eeur_669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.92 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETSAGKHVPRAVFVDLEP
          ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDK..G.GDDSFNTFFSET.AGK.VPRAVFVDL.P
Retrocopy ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKFTGNGDDSFNTFFSETGAGKLVPRAVFVDLQP

Parental  TVIDEVRTGTYRQLFHPEQ-LITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLADQCTGLQGFLVFHSF
          .VIDE...G.YRQLFHP....ITGKEDAANNY..GHYT.G.EIID.V.DRIR..A.QCTGLQ.FLVFHSF
Retrocopy IVIDEIHKGPYRQLFHPDN<FITGKEDAANNYVCGHYTLGREIIDHVSDRIRTVAHQCTGLQDFLVFHSF

Parental  GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQ-VSTAVVEPYNSILTTHTTLEHCDCAFMVDNEAIY
          GGG.G.GFT.LLME.L.VDYG.K.KLEFSI.PA...VSTAVV.PY.SILTTH.TLEHCDCAFMVDNEAIY
Retrocopy GGGAGFGFTFLLMECLCVDYGRKFKLEFSICPASR<VSTAVVKPYSSILTTHSTLEHCDCAFMVDNEAIY

Parental  DICCRNLDIERPTYTNLNRLISQVVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          DIC.RNLDIERPTY.NLN.LISQVVSSITASLRFDGALNVDL.E.QTNLVPYP.IHFPL.TYA..ISAEK
Retrocopy DIC*RNLDIERPTYINLNHLISQVVSSITASLRFDGALNVDLAELQTNLVPYPHIHFPLTTYALAISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIASIKTKRTIQFVDWCPTG
          AYH.Q.SV.E.TN.CFE.ANQMVKCDPR.GKYMACCLL..GDVVPKDV.AAIASIKTK..IQFVDW.P.G
Retrocopy AYHQQFSVLEFTNVCFESANQMVKCDPRYGKYMACCLLHHGDVVPKDVSAAIASIKTKHSIQFVDWYPAG

Parental  FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAVAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFAE
          FKV.INYQPPTVVPGGDLAKV..AVCMLS.TT..AEAWARL.HKFDL..AK.AFVHWYVGEG..EGEF.E
Retrocopy FKVDINYQPPTVVPGGDLAKVEWAVCMLSKTTVIAEAWARLKHKFDLLFAKCAFVHWYVGEGIGEGEFSE

Parental  AREDMAALEKDYEE-VGADSADGDDEGE
          AREDMA.LEKDYEE.VGADSA.GD...E
Retrocopy AREDMATLEKDYEE<VGADSAAGDENPE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	52.05 RPM
SRP017611_kidney	0.00 RPM	60.20 RPM
SRP017611_liver	0.00 RPM	84.73 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_669 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Erinaceus europaeus	ENSEEUG00000004068	1 retrocopy	retro_eeur_669 ,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
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,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,