RetrogeneDB ID: retro_itri_203

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393279.1:28665490..28666719(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA4A
• Ensembl ID: ENSSTOG00000019497
• Aliases: None
• Description: tubulin, alpha 4a [Source:HGNC Symbol;Acc:12407]

Sequence

>retro_itri_203
ATGCGTGAGTGTATCTCAGTTCATGTGGGGCAAACAGGTGTCCAGATGGGCAATGCCTAATGGGAGCTCTACTGCCTGGA
ACATGAGATTCAGCCTGATAGCCAAATACCCAGTGACAAGACTATTGGTAGAGGGGACACCTCCTTCACCACCTTCTTCT
GTGAAACTGGTGCTGGAAAACATGTGCCCAGAGCCATCTTTGTGGACCTGGAGCCCACTGTAATTGATGAGATCCGAGAT
GGCCCATACCGAAAGCTCTTCCACCCAGAGCAGCTCATCACTGGGGAAAGAGGATGCTGCTAACAACTATGCCCGTGGCC
ATTACACCATTGGCAAGGAAATCATTGACCCTGTAATCGACCGGATCCTCAAGCTGTCTGACCAGTGCACAGGACTTCAA
GGCTTCCTGGTATTCCACAGTTTGGAGGGGGCACCAGCTCTGGCTTCAACTCCCTCCTGATGGAGCGGCTCTCTGTGGAC
TATGGCAAGAAATCCAAGCTGGAGTTCTCCATCTACCCAGCCCCTCAGGTGTCCACAGCCGTGGTGGAGCCCTACAACTC
CATCCTGACCACCCACACGACCCTGAAGCACTCAGACTGTGCCTTCATGGTGGACAACGAGGCCATCTATGACATCTGCC
ACCACAACCTGGACATCGGTGCCCAACCTACACCAACCTCAACCGCCTCATCAGCCAAATCGTGTCCTCCATCACAGCTC
CCCTGTGTTTCGATGGGGCCCTCAACGTGGACCGGACGGAGTTCCAGACCAACCTGGTGCCCTGCCTGCGCATCCACTTC
CCCCTGGCCACCTATACGCCAGTCATCTCTGCAGAGAAGGCCTACCACGAGCAGCTGTCAGTGGCAGAAATCACCAAGGT
CTGCTTTGAGCCTGCCAACCATATGATGAAGCATGACCCCCGGCATGGCAAGTACATGGCCTGCTGCCTGCTGTACCGTG
GAGACGTGGTGCCCAAAGATGTCAATGCCGCCATTGCTGCCATCAAGATCAAGCGTAGCATCCTGTTTCTGGACTGGTGC
CCCACAGGCTTCAAGGTTGGCATCAACTATCAGCCTCCCACTGTGGTGCCTGGGGGAGACCTGGCCAAGGTGTAGCGTGG
TGTGTGCATGCTGAGCAACACGACCGCCATCGCCGAGGCCTGGGCCCGCCTGGACCACAAGTTCAACCTGATGTATGCCA
AGAGGGTGTTTGTGCACTGATACGTGGGT

Alignment

ORF - retro_itri_203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.07 %
• Parental protein coverage: 91.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDL
          MRECISVHVGQ.GVQMGNA.WELYCLEH.IQPD.Q.PSDKTIG.GD.SFTTFFCETGAGKHVPRA.FVDL
Retrocopy MRECISVHVGQTGVQMGNA*WELYCLEHEIQPDSQIPSDKTIGRGDTSFTTFFCETGAGKHVPRAIFVDL

Parental  EPTVIDEIRNGPYRQLFHPEQLITG-KEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGLQGFLVFH
          EPTVIDEIR.GPYR.LFHPEQLITG.KEDAANNYARGHYTIGKEIIDPV.DRI.KLSDQCTGLQGFLVFH
Retrocopy EPTVIDEIRDGPYRKLFHPEQLITG>KEDAANNYARGHYTIGKEIIDPVIDRILKLSDQCTGLQGFLVFH

Parental  S-FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEA
          S.FGGGT.SGF.SLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTL.HSDCAFMVDNEA
Retrocopy S<FGGGTSSGFNSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLKHSDCAFMVDNEA

Parental  IYDICRRNLDIER-PTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVIS
          IYDIC..NLDI...PTYTNLNRLISQIVSSITA.L.FDGALNVD.TEFQTNLVP..RIHFPLATY.PVIS
Retrocopy IYDICHHNLDIGA<PTYTNLNRLISQIVSSITAPLCFDGALNVDRTEFQTNLVPCLRIHFPLATYTPVIS

Parental  AEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIAAIKTKRSIQFVDWC
          AEKAYHEQLSVAEIT..CFEPAN.M.K.DPRHGKYMACCLLYRGDVVPKDVNAAIAAIK.KRSI.F.DWC
Retrocopy AEKAYHEQLSVAEITKVCFEPANHMMKHDPRHGKYMACCLLYRGDVVPKDVNAAIAAIKIKRSILFLDWC

Parental  PTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVG
          PTGFKVGINYQPPTVVPGGDLAKV.R.VCMLSNTTAIAEAWARLDHKF.LMYAKR.FVH.YVG
Retrocopy PTGFKVGINYQPPTVVPGGDLAKV*RGVCMLSNTTAIAEAWARLDHKFNLMYAKRVFVH*YVG

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_203 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_203 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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,