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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagttttatcttattcctatgcgcatagtgtttgattatatatatgtgttaatgttgaataattttttctgcaatagctcacattgacaagctaattg...

Basic information

species Glycine max
transcript GLYMA08G09180.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G152757_T01 (Zea mays), 5'ss of exon 2
AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttt--atcttattcctatgcgcatagtgtttgattatatatatgtgttaatgttgaataattttttctgcaatagctcacattgacaagctaattg
| ||| ||  ||| | || |||| || |  || ||  | ||| |||||||||||||||||||||||||||||||||||  ||  |  || ||||    |      || || |||||  | | |  ||   |      |||    ||  || ||| |||  |  ||   ||   || | 
ACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgtacgtgctggattttatcttcaattctgta-tgattgatgcttt-tgagttgcatccacaaatccaattcgctccaaaagcaaagtttctgaacaaaaatc

upper sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G63980.1 (Arabidopsis thaliana), 5'ss of exon 2
AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagttt--tat-cttattcctatgcgcatagtgtttgattatatatatgt-gttaatgttg------aataattttttctgcaatagctcacattgacaagctaattg
||||| || |||||| |  ||||||| |||||||| ||||| || || |||||||| || || || ||||||||||||||||||  ||| | | | |||      | |  | |    | | |  ||||   | |  |||      ||| | ||  | ||   |  ||    |||| |    |    
AAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATGgttagtttgttatacctgtccctgattagaaaaagctcttctctttgaatgttactgagattgttaggaaatcacttaatttgatctgtcttgtgttga-atttcag---

upper sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 5'ss of exon 2
AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagttttatcttattcctatgcgcatagtgtttgattatatatatgtgttaatgttgaataattt--tttctgcaatagctcacattgacaagctaattg--
||||| || ||||| ||  ||||||| ||||| || || || ||||| ||||| ||||||||||||||||| ||||||| ||   |||||||||   ||| |||    ||  | |||||  || |  |  | |    |   ||  ||  ||  ||   | | |  | |||     ||   
AAAGTGCAAAAGGCGCTGTTGCAATCAGATGTCCAATCTAAATCAGATAAAAGCCCTGTCACAGTGGCTGACTATGgtttgt---atcttattcacctgcacatttatttcaactatattgatat-ctgctatcagctctcttagttgttgttattaatgataggggcaattgtgttttg

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|192323419|gb|FK015305.1|FK015305
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|193665926|gb|FK611313.1|FK611313
EST:     GACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: GACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|21677711|gb|BQ630062.1|BQ630062
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|192311655|gb|FK004874.1|FK004874
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|298190692|gb|HO032813.1|HO032813
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GCTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|209712035|gb|BW674180.1|BW674180
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|192311684|gb|FK004875.1|FK004875
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|24205274|gb|BU964527.1|BU964527
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|7587871|gb|AW703678.1|AW703678
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|37996739|gb|CF808328.1|CF808328
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|298163506|gb|HO012239.1|HO012239
EST:     TGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|16996758|gb|BM086130.1|BM086130
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|208159325|gb|GD955242.1|GD955242
EST:     CAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|8285675|gb|BE023234.1|BE023234
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
EST: gi|6566797|gb|AW234429.1|AW234429
EST:     CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG                         GTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC
genomic: CGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagtttta ... tggtttacagGTTCACAAGCATTGGTCAGCTTTATACTTGAGAGAGAACTTCCTTCTGAAC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagttttatcttattcctatgcgcatagtgtttgattatatatatgtgttaatgttgaataattttttctgcaatagctcacattgacaagctaattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT