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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgcttaatgatctcttctagttaaagttggaaaaaagtttttaagtatacagtggaaaagactaatgaaataactcctatttgtctcgttttgggt...

Basic information

species Glycine max
transcript GLYMA04G42010.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42010.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os12g08830.2 (Oryza sativa), 5'ss of exon 2
GAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgat--gcttaa--tgatctcttctagttaaagttggaaaaaagtttttaagtatacagtggaaaagactaatgaaataactcctatttgtctcgttttgggt
||| || || || ||||| || || ||||| || |||||||| ||||||||||| || || ||||| |||||||||| ||| | ||| |  |||||||||||||    || ||  |  | ||    | | | | ||  | || | | |   | | |         || | | |||   |   ||| ||||   ||  | | |  
GAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGAAGAGgtgaaaaactgaagctactgtcacaaattcagatttatagaacactgtcacaatctttccgatgcaaaattgatgctgt---tccaattt--ttcaatgtag--

upper sequence: GLYMA04G42010.1 (Glycine max), 5'ss of exon 2
lower sequence: AT1G77090.1 (Arabidopsis thaliana), 5'ss of exon 2
GAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgcttaatgatctcttctagttaaagttggaaaaaagtttttaagtatacagtggaaaagactaatgaaataactcctatttgtctcgttttgggt
||| || || || || || || |||||||||||||| ||||||||||| |||||||||||||| || |||  |||    || ||| |||| ||| | |||||  ||     ||     |  |  ||    |      |  |||||||   ||||  ||  |     |       |   ||  ||||              
GAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAATGAGgttttgtcccttggctcttgtttcttcgtttct----atggtttttagtcatactttgagattcttttcattgttgtatcaaatttag------------

upper sequence: GLYMA04G42010.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0001g15360.t01 (Vitis vinifera), 5'ss of exon 2
GAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgcttaatgatctcttctagttaaagttgg-----aaaaaagtt---tttaagtatacagtggaaaagactaatgaaataactcctatttgtctcgttttgggt-----------
|||||| || || || |||||||| || || ||||| |||||||||||||||||||| |||||||| |||| |||   ||| |||   |  ||||||||||| ||  |  |    | ||      || | | |      | |    ||   |||     | |   |  |   ||   |   | || | |      |    || | | |           
GAGGACATACCGGAGACCGGATGAAAAATCTGGAGGCCATGGTGTTGGATGGAGTCCGATTATTCCTTACATCTTTTCAGTCCCTTCTGGTTGGGAAGAGgtaataatctacctccactggactatagactcgacccctatattgattcattttcccccttcctggacatctacctctaccacaatttcaccaaataagcttcttgatccatgtcacag

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|151399188|gb|EV269059.1|EV269059
EST:     GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
genomic: GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
EST: gi|24205729|gb|BU964982.1|BU964982
EST:     GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
genomic: GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
EST: gi|15285767|gb|BI469658.1|BI469658
EST:     GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
genomic: GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
EST: gi|5509839|gb|AI856397.1|AI856397
EST:     GNAGTCCTATTATTCCATACAGCTTCAGAGTGCNTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATNTGAGATTT
genomic: GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
EST: gi|209716366|gb|BW657486.1|BW657486
EST:     GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
genomic: GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
EST: gi|151397074|gb|EV266947.1|EV266947
EST:     GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
genomic: GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
EST: gi|31469528|gb|CD411556.1|CD411556
EST:     TTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
genomic: TTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
EST: gi|151402608|gb|EV272421.1|EV272421
EST:     GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGC
genomic: GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGC
EST: gi|5510308|gb|AI856750.1|AI856750
EST:     GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
genomic: GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTT
EST: gi|213594235|gb|DB966136.1|DB966136
EST:     GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAG                         GTACCAGTATCAATAGC
genomic: GGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgctta ... tgcttaacagGTACCAGTATCAATAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGAAGAGgtgatgcttaatgatctcttctagttaaagttggaaaaaagtttttaagtatacagtggaaaagactaatgaaataactcctatttgtctcgttttgggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaga