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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataaccgatatttgcatgctctgttcacaattcttgaactttgagatgataggaagcctgaaatagtgtttaacgttgactaatacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG

Basic information

species Arabidopsis thaliana
transcript AT4G38510.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
---gtgataaccgatatttgcatgctctgttcacaattcttgaactttgagatgataggaagcctga-aatagtgtt--taacgttgactaatacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG
    |  | | |  | |||    |  || |  | | |   | |   ||  |   | |   ||  ||| ||| |   |  | ||     ||    ||  ||||| ||||||||||| |||||||| ||||| || ||||| ||||| ||||||||||| || ||  | || || ||||||||  | || ||  ||||||| |
catttatttatctctttttctccga-ctataaaaagtaactaagtattttgcaaacaattagattgacaatggaactattgaccccttctggatcctgtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------------------------gtgataaccgatatttgcatgctctgttcaca-attcttgaactttgag--atgataggaagc-ctgaaatagtgtttaacgttg-actaatacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG
                                                                                     | | ||  || |||    |   |  ||     ||||||| | | ||||  || |  | ||    |   |||    ||  | |   |||    ||| ||||| ||||||||||| ||||||||||| ||||| |||||||| || || || ||||| || ||  | || || || || ||  |||| ||| ||||||| |
gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttataggctttaatgatgatttaaaattgacattcttttatgcctttggtttattcttggagtatgagaaataactgaaaatatttctataacaatttgcatgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EDP06821 (Chlamydomonas reinhardtii), 3'ss of exon 7
-----------------------gtgataaccg-atatttgcatgctctgttcacaattcttgaactttgagatg-ataggaagcctgaaatagtg-----tttaacgttgactaataccctta---gGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG----------------------------------------------
                       | | |   |      | ||  ||   ||  |     | ||  || |  | ||     |   || |  |    |     |    ||  |   |    ||||    ||    |||| ||  |||    ||  |           |||   |||||||||||||||| |||||||| ||||| |||||| | || || || || || |                                              
gtgagcacgagctgggatgctgggcgctgcgcacgcggtggcgcgcggggtgtaggtgccgtgcgctctagggtgtgcgcgtcacccgtgacgacggagactcgggcggcgcagaggggccttgaacggaagatgcttccgctgactttgtatcaactccttcgcgttcaacagGTTACATGTACACTGACTTGGCCACCATCTACGAGCGCGCCGGCCGTATCGAGGGCCGCAAGGGCTCCATCACGCAGCTGCCCATTCTTACCATGCCCAA

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------------------------------------------------------gtgataaccgatatttgcatgctctgttcacaattcttgaactttgagatgataggaagcctgaaatagtgtttaacgttgactaatacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG
                                                                                                    ||  | |   | ||||| |  || |        || || |   || |||   |  |    ||  ||   | ||  ||  | | |  | |   ||||| |||||||| |||||||||||||||||  | ||||| || || ||||||||||| || ||  |||| ||||| || ||  | || || ||||| ||||
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaa---ttaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

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|86066802|gb|DR362559.1|DR362559
EST:     TCCTTGTCATTCTCACAGACATGAGTTCCTACGCCGATGCTCTTCGTGAG                         GTCTCTGCTGCCCGTGTNNA-GTGCCTGGANNGCGTGGTTACCCCAG-TTA
genomic: TCCTTGTCATTCTCACAGACATGAGTTCCTACGCCGATGCTCTTCGTGAGgtgataaccg ... atacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCC-AGGTTA
EST: gi|116450403|gb|EG492995.1|EG492995
EST:     GACATGAGTTCCTACGCCGATGCTCTTCGTGAG                         GTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTAC
genomic: GACATGAGTTCCTACGCCGATGCTCTTCGTGAGgtgataaccg ... atacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTAC
EST: gi|124911447|gb|EH985527.1|EH985527
EST:     TCCTTGTCATTCTCACAGACATGAGTTCCTACGCCGATGCTCTTCGTGAG                         GTCTCTGCTGCCCGTGAAGAAGTGCCT
genomic: TCCTTGTCATTCTCACAGACATGAGTTCCTACGCCGATGCTCTTCGTGAGgtgataaccg ... atacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCT
EST: gi|116450411|gb|EG493003.1|EG493003
EST:     TCCTTGTCATTCTCACAGACATGAGTTCCTACGCCGATGCTCTTCGTGAG                         GTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTGC
genomic: TCCTTGTCATTCTCACAGACATGAGTTCCTACGCCGATGCTCTTCGTGAGgtgataaccg ... atacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTAC
EST: gi|116476764|gb|EG519356.1|EG519356
EST:     TCCTTGTCATTCTCACAGACATGAGTTCCTACGCCGATGCTCTTCGTGAG                         GTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTAC
genomic: TCCTTGTCATTCTCACAGACATGAGTTCCTACGCCGATGCTCTTCGTGAGgtgataaccg ... atacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttgagatgataggaagcctgaaatagtgtttaacgttgactaatacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG
                                        gactaat  putative branch site (score: 2)
                                              taccctt  CT-rich tract
                     tgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgataaccgatatttgcatgctctgttcacaattcttgaactttgagatgataggaagcctgaaatagtgtttaacgttgactaatacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG