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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattctatgcacaatgccttaagatattagtttagtttcatgcattataggtgttttaaaaatttgacattgagcttttgtttaatttgttttaatctag

Basic information

species Glycine max
transcript GLYMA13G22720.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G22720.1 (Glycine max), 5'ss of exon 22
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 5'ss of exon 22
AGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattctatgcacaatgccttaagatattagtttagtttcatgcattataggtgttttaaaaatt-tgacattgagcttttgtttaatttgttttaatctag
||| || |||||| | ||||| |||||||||||||| ||||| ||||| || ||||||||||||||||| || ||||| ||||||||| | || ||||||||||| || ||| |   | || |    |||||   | | | || |   | ||| |       ||  |  |  | || |  ||  || |      |||| |     
AGCAGCAACATTTTTGGCATTCCATCCTCAAGACAATAATATCATTGCCATAGGCATGGAGGACTCTTCTATCCAAATATATAATGTTCGGGTTGACGAGgtattctt-tattc-tgaagctt----atattttgtgattctctttgttgataagcaggcagaagttgatatcgttcaaattgggtatgccacattttgacag--

upper sequence: GLYMA13G22720.1 (Glycine max), 5'ss of exon 22
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 21
AGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtat--tat----tctatgcacaatgccttaagatatta-gtttagtttca--tgcatt-ataggtgttttaaaaatttgacattgagcttttgttta---atttgttttaatctag-------------
||| ||||| ||||||||||||||||| |||||||||||||| |||||||| || ||||| || ||  | || || || ||||||||| | ||||| |||||||  |||    ||  |||   ||   ||  | | ||  | || ||  ||  ||  || ||   | | |      ||| | ||    || | ||| |     ||  |   || |               
AGCAGCTACTTTTCTTGCATTTCATCCACAAGACAACAATATCATTGCTATCGGAATGGAAGATTCGACAATTCAGATTTATAATGTTCGTGTGGATGAGgtatgttatcaagtccttgccagataagttgcgcttttgtgatttgtcacacttgtgttgatgcatatgtctcggttttaatataagactgtcgttgatacgcttaataagatttctctgctgttcacag
















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|192302428|gb|FG995912.1|FG995912
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattct ... tttaatctagGTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
EST: gi|11412135|gb|BF424146.1|BF424146
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattct ... tttaatctagGTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
EST: gi|7795165|gb|AW780562.1|AW780562
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTTGAGTGGACGAT                         GTCAAAACTAAGCTAAAGGGTCATCAGAAGAGA-TTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattct ... tttaatctagGTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
EST: gi|6201163|gb|AW153263.1|AW153263
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattct ... tttaatctagGTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
EST: gi|16349478|gb|BI975073.1|BI975073
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACCAAGCTAAAAGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattct ... tttaatctagGTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
EST: gi|14990529|gb|BI316202.1|BI316202
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACCAAGCTAAAAGGTCATCAGAAGAGAATTAC
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattct ... tttaatctagGTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTAC
EST: gi|208204121|gb|GE006954.1|GE006954
EST:     TTGGCATGGAGGACTCTTCCATACAAATC-ATAATGTTAGAGTGGACGAG                         GTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattct ... tttaatctagGTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
EST: gi|6482921|gb|AW202189.1|AW202189
EST:     TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAG                         GTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT
genomic: TTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattct ... tttaatctagGTCAAAACTAAGCTAAAGGGTCATCAGAAGAGAATTACTGGTCTTGCCTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGCTACATTTCTTGCATTTCATCCTCAAGACAACAATATTATTGCTATTGGCATGGAGGACTCTTCCATACAAATCTATAATGTTAGAGTGGACGAGgtattattctatgcacaatgccttaagatattagtttagtttcatgcattataggtgttttaaaaatttgacattgagcttttgtttaatttgttttaatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA