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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaacaaaacatttcttttttctgaactatgcctttgtttttgtttttgtttttgcttagactcatctttctattgttctctttggtatcag

Basic information

species Arabidopsis thaliana
transcript AT4G02840.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 5'ss of exon 3
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaaca-aaacatttcttttttctgaactatgcctttgtttttgtttttgtttttgcttagactcatctttctattgttctctttggtatcag
|||||||||||||||||||| |||||||| ||||| || || |||||||| ||||||||||| || || || ||  ||||  | || |||||||||||||||   | ||   |||  | | ||| |  |     |       || |    | ||||  |   |  | |||  |   |                
GGAAACAACATTCGCTATTACATTCTTCCTGACAGCTTAAACCTGGAGACATTGCTGGTTGAGGATACACCGAGGGTCAAGGCTAAGAAGCCAACTGCAGgtttgataattgttttgtctctctaagttgattttactgagctgctgaactgtttgtctgatcaaaccttaatccggaaacag----------

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G416061_T01 (Zea mays), 5'ss of exon 4
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaacaaaacatttcttttttctgaactatgcctttgtttttgtttttgtttttgcttagactcatctttctattgttctcttt--ggtatcag
||||||||||| ||||||||||| ||||| |||||  | || |||||||||||||||||||| || || |||||  |||| || || ||||| ||| | ||| | |     ||  |||| ||  |  |   |||| |     | |||      |||| ||  | ||| ||  ||   |||   |     | |||
GGAAACAACATCCGCTATTATATCCTTCCTGACAGCCTAAACCTGGAGACTTTGCTGGTTGAGGAAACACCAAGGGTCAAGCCTAAGAAGCCTACTTCTGgtcagag----ttctttttctcccatttcaaccttcga----gatttaccacctgct-agcattatcatttcatccatcttcatcaaaaaccag

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G30880.1 (Glycine max), 5'ss of exon 3
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgta--acaaaacatttc-ttttttctgaactatgcctttgtttttgtttttgtttttgcttagactcatctt----tctattgttctc-----tttggtatcag------
|| ||||||||||| |||||||| ||||| ||||| |||||||| |||||||| |||||||||||  |||| |  ||||| || || ||||||||||| ||||    | |  ||||   | |  || || | |   |  |   ||  || ||||   | | |   | |||      | | | ||||||     |||| | | |       
GGCAACAACATTCGATATTATATCCTTCCTGACAGCTTGAATCTTGAGACTTTACTGGTTGAAGAGGCTCCTAAGATCAAGCCTAAGAAGCCAACTGCTGgtattgtatattatttgactgtcactaaaatgtttatcagaagttaattatgttcaggttgactgttatcaagggatatctggttctcaaagttttgattttatttgcag

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G33700.1 (Glycine max), 5'ss of exon 3
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgta--acaaaacatttc-ttttttctgaactatgcctttgtttttgtttttgtttttgcttagactcatctt----tctattgttctc-----tttggtatcag------
|| ||||||||||| |||||||| ||||| ||||| |||||||| |||||||| |||||||||||  |||| |  ||||| || || ||||||||||| ||||    | |  ||||   |||  ||  | | |   |  |       || ||||   | | |   | ||||     | | | ||||||     |||| | | |       
GGCAACAACATTCGATATTATATCCTTCCTGACAGCTTGAATCTTGAGACTTTACTGGTTGAAGAGGCTCCTAAGATCAAGCCTAAGAAGCCAACTGCTGgtattgtatattatttgactttcactagaatgtttatcagaggccaattatgttcaggttgactgttatctaggaatatctggttctcaaagttttgattttatttacag

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G10640.1 (Glycine max), 5'ss of exon 4
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgta-----------------acaaaacatttcttttttctgaactatgcctttgtttttgtttttgtttttgcttagactcatctttctattgttctctttg--gtatcag
|| |||||||| || || ||||||||||| ||||| |||||||| ||||| |||||||| ||||| || || |  ||||||||||| ||||||||||| ||||                 ||||||  ||  |   | || || |    ||   | ||| ||  ||  ||  |   |  | |  |||    | || || ||    |  |||
GGTAACAACATCCGTTACTATATTCTTCCTGACAGCTTGAATCTTGAGACCTTGCTGGTGGAAGAGACACCCAAGATCAAACCCAAGAAGCCAACTGCTGgtactgtttatagtttgactacaaaattttcatccatactcaattcactctaattgtttcttggtgagttccccaggttttaattttagcatattttcattacatttccag

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA18G52210.1 (Glycine max), 5'ss of exon 4
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaaca-aaacatttcttttttctgaactatgcctttgtt---tttgtttttgtttttgcttagactcatctttctattgttctctttggtatcag-----------------
 | |||||||| || || || |||||||| ||||| |||||||| |||||  |||| || ||||| || || |  ||||||||||| ||||||||||| ||||    | | | ||    |     |  ||   |  || |   ||  || |  || || ||| |     |   ||   | |  | |||   ||                    
-GTAACAACATCCGTTACTACATTCTTCCTGACAGCTTGAATCTCGAGACCCTGCTTGTGGAAGAGACACCTAAGATCAAACCCAAGAAGCCAACTGCTGGtactgtatatagtttaactacaaaatttacatccatgctcaattcattctaattgtttcttgg-tgagttcctcaggtttaatttttaacatattttcatcgcatttccagg

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 5'ss of exon 5
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaacaaaacatttcttttttctgaa--ctatgcctttgtttttgtttttgtttttgcttagactcatctttct-attgttctctttggtatcag
|| ||||||||||| |||||||| ||||| ||||| |||||||| |||||  |  |||| ||||| || || ||  |||| ||||| |||||||| |||||||       || |||||      ||  |||||| |||   | || |||   ||   |||    | || ||| | | || | | ||   | ||||
GGCAACAACATTCGGTATTATATCCTTCCCGACAGCTTGAATCTTGAGACCCTTTTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACCGCAGgtattgctctatctctttggctctaattctatgcattttcgtatgatttatgttccccttgttttaattttttttaatgcttttttccatttcag

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 5'ss of exon 3
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaacaaaacatttcttttttctgaactatgcctttgtttttgtttttgtttttgcttagactcatctttctattgttctctttggtatcag
|| ||||| ||||| |||||||| ||||| |||||  | ||||||||||| |||||||| ||||| || || ||  |||| ||||| ||||||||||| ||||      ||| | |   || |||  |||     |  |  |   ||  |  ||  | | | |  | ||| || ||  |||| |     |||
GGCAACAATATTCGGTATTATATACTTCCCGACAGCATAAATCTGGAGACATTGCTGGTGGAAGAGACACCTAGGGTCAAGCCCAAGAAGCCAACTGCTGgtatt---gcatatttcccttttgacttatataccttgtgatagattaatactttttaaaatt--tttttttaatgc-ctctataaatccag

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|164159770|gb|ES005818.1|ES005818
EST:     GAAGACACTCCAAGAATCAAACCCGAAAAGCCAACTGCAG                         GTAAGATTCCAGCAGGTCGGGGACGTGGTCGTGGAAGAGGT
genomic: GAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaacaaaac ... ttggtatcagGTAAGATTCCAGCAGGTCGGGGACGTGGTCGTGGAAGAGGT
EST: gi|164004850|gb|ES161662.1|ES161662
EST:     TCCAAGAATCAAACCCAAAAAGCCAACTGCAG                         GTAAGATTCCAGCAGGTCGGGGACGTGGTCGTGGAAGAGGTCGTGGACGTG
genomic: TCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaacaaaac ... ttggtatcagGTAAGATTCCAGCAGGTCGGGGACGTGGTCGTGGAAGAGGTCGTGGACGTG
EST: gi|19798186|gb|AU229706.1|AU229706
EST:     TTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAAGCCAACTGCAG                         GTAAGATTCCAGCAGGTCGGGGACGTGGTCGTGGAAGAGGTCGTGGACGTG
genomic: TTGCTGGTTGAAGACACTCCAAGAATCAAACCC-AAAAAGCCAACTGCAGgtaacaaaac ... ttggtatcagGTAAGATTCCAGCAGGTCGGGGACGTGGTCGTGGAAGAGGTCGTGGACGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAACAACATTCGCTATTATATTCTTCCGGACAGTTTGAATCTGGAGACTTTGCTGGTTGAAGACACTCCAAGAATCAAACCCAAAAAGCCAACTGCAGgtaacaaaacatttcttttttctgaactatgcctttgtttttgtttttgtttttgcttagactcatctttctattgttctctttggtatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG