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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaactttggcgcaatgttagttgtttgaatcactgtgtcgtgcttagttttttatggacttatttgtggtttgtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG

Basic information

species Arabidopsis thaliana
transcript AT3G44200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 6
gtaaaaactttggcgcaatgttagttgtttga--atcactgtgtcgtgctt--agttttttatggacttatttgtggtttgtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
||| |    |  |    |  |||  || |  |  ||   ||| |     ||  | | | ||| |      ||||| |  | |  |  |||||||||||||| || ||||| |||||||| |||||||||||||
gtatacttgtatgaattaaattatatggtctatgattcttgtctttcatttgaaatgtattaagtctgattttgttgactctgttgacagTGTTCCAACATCTTTCTTACCAAAGATCAGGATGTTCGCCTTG

upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 6
--------gtaaaaactttggcgcaatgttagttgtttga--atcactgtgtcgtgctt--agttttttatggacttatttgtggtttgtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
        |||  || ||   |   |||| |  || |  |  ||   ||| |     ||  | ||| ||| |      ||||| | || |  |  |||||||||||||| || ||||| ||||||| |||||||||||| |
gtatacttgtatgaa-ttaaactatatgtaatatggtctatgattcttgtctttcatttgaaatttattaagtctgattttgttgattctgttgacagTGTTCCAACATCTTTCTTACCAAAGATCGAGATGTTCGCCTAG
















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|86062641|gb|DR358398.1|DR358398
EST:     TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAG                         TGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
genomic: TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAGgtaaaaactt ... gtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
EST: gi|86062640|gb|DR358397.1|DR358397
EST:     TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAG                         TGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
genomic: TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAGgtaaaaactt ... gtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
EST: gi|86062638|gb|DR358395.1|DR358395
EST:     TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAG                         TGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
genomic: TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAGgtaaaaactt ... gtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
EST: gi|86062636|gb|DR358393.1|DR358393
EST:     TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAG                         TGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
genomic: TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAGgtaaaaactt ... gtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
EST: gi|86062639|gb|DR358396.1|DR358396
EST:     TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAG                         TGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
genomic: TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAGgtaaaaactt ... gtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
EST: gi|86062637|gb|DR358394.1|DR358394
EST:     TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAG                         TGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
genomic: TAGCTGTTGAGTATCTGCATTCTAACTATGTTCTACATCGGGATCTAAAGgtaaaaactt ... gtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcactgtgtcgtgcttagttttttatggacttatttgtggtttgtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG
                                              tacttcc  CT-rich tract
                ttagttttttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaactttggcgcaatgttagttgtttgaatcactgtgtcgtgcttagttttttatggacttatttgtggtttgtacttccagTGTTCCAACATTTTCCTTACAAAAGATCAAGATGTTCGCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG