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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctatctcattcgtcaaaaagcttgttttgattctctgatgattatgcttaatcttcattctctgattgttcttttgtttttcaattgttattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA

Basic information

species Arabidopsis thaliana
transcript AT5G46430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G46430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g41300.1 (Oryza sativa), 3'ss of exon 2
at-ctatctcattcgtcaaaaagcttgttttgattctctgatgattatgcttaatcttcattctctgattgttcttttgtttttcaattgttattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA
||  |||  | ||| | |    || ||   |  |  | || | | ||||  || |   |||  |      |      |     |   |  |  |||| |||  ||||||| | ||||| ||||||||||||||||| || || ||||||||||||||   |||||||||||||||  |||||||||| || || |||||||
atgttattgctttcattagtgggcatggcatcctcgtttg-taactatggctatttggcatatttgctgagactaacttcaacttgttcatacttgtccagCCAAGCTGGCGCAGGCCCAAGGGTATTGACTCCCGTGTCAGGAGAAAGTTCAAGGGATGCACCTTGATGCCCAACATTGGTTACGGCTCAGACAAGAAGA

upper sequence: AT5G46430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g32500.1 (Oryza sativa), 3'ss of exon 2
--atctatctcattcgtcaaaaagcttgttttgattctctgatgattatgcttaatcttcattctctgattgttcttttgtttttcaattgttattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA
   | ||||   |||       | | |  |       | |  ||    |  ||  |  |         |  | || |||   |||  | ||||  |||  ||  ||||||| | ||||| |||||||||||||| || || || ||||||||||| ||   |||||||||||||||  |||| || || ||||| |||||||
ttttatatcgttttcagtctgcatcctagtcacgccatgtattgtcagtttttgtttgtgtggacacaagggctcattttcatttgcactgtttctgt--agACAAGCTGGCGCAGGCCAAAGGGTATTGACTCTCGTGTCAGGAGAAAGTTCAAAGGATGCACCTTGATGCCCAACATTGGATATGGTTCTGACAAGAAGA

upper sequence: AT5G46430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g32532.2 (Oryza sativa), 3'ss of exon 1
atctatctcattcgtcaaaaagcttgttttgattctctgatgattatgctta-atcttcattctctgattgttcttttgtttttcaattgttattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA
 |     | ||| ||    ||  |   |    ||||| | | |||    ||   |  |   |  || |   ||  | |  |||| | ||     | |  ||  ||||||| | ||||| |||||||| |||||||| || || ||||||||||||||   ||| |||||||| ||| |||| || || ||||| |||||||
-tgctgatgatttgtttctaacttgaatacacttctccgcttatttcttttgtgtgctgccttgcttaaatttggtgttctttttacttccctatatgtagACAAGCTGGCGCAGGCCAAAGGGTATCGACTCCCGTGTCAGGAGAAAGTTCAAGGGATGCACTTTGATGCCTAATATTGGCTATGGTTCTGACAAGAAGA

upper sequence: AT5G46430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: AC197246.3_FGT003 (Zea mays), 3'ss of exon 1
atctatctcattcgtcaaaaagcttgttttgatt---ctctg-atgattatgcttaat-cttcattctctgattgttcttttgtttttcaattgttattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA
   |   |  ||   | | |   |||| || ||    ||||  || |||||   |||| ||  |||||       |   | ||  | |  ||||||  ||| |||  ||||||| | ||||| ||||||||||||||||| || || || |||||||||||   |||||||||||||||  |||||||||| ||||| ||    |
---tggatgtttaacccatatctttgtgtttatctccctctatatcattatctataattctatattctagaggactaactatgactgtttattgtt--tgtacagCCAAGCTGGCGCAGGCCAAAGGGTATTGACTCCCGTGTCAGGAGGAAGTTCAAGGGATGCACCTTGATGCCCAACATTGGTTACGGCTCTGACAAATCAA

upper sequence: AT5G46430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G155931_T03 (Zea mays), 3'ss of exon 1
atctatctcattcgtcaaa-aagcttgttttgattctctgatgattatgc-ttaatcttcattctctgattgttcttttgtttt--tcaattg--ttattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA
        ||  | || |   ||||||||||  || |   ||   | ||  || || | | | |   || |  |  |  ||| |      |||  |  |||| |||  ||||||| | ||||| ||||||||||||||||| || || || |||||||||||   |||||||||||||||  ||||||| || ||||| |||  ||
------tgcagacatctattgagcttgtttttcttataccatttctttgtatttatttccctccatagagtaattctaagttctgacttgttgattctttgtacagCCAAGCTGGCGCAGGCCAAAGGGTATTGACTCCCGTGTCAGGAGGAAGTTCAAGGGATGCACCTTGATGCCCAACATTGGTTATGGTTCTGACAAGTCGA

upper sequence: AT5G46430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G047971_T01 (Zea mays), 3'ss of exon 2
atctatctcattcgtcaaaaagcttgttttgattctctgatgattatgcttaatcttcattctctgattgttcttttgtttttcaattgt-tattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA
 |       || |   |||| | |||       | ||   |     ||| ||| | |  |   ||  |||    |   |||  | ||  | | ||||  ||  ||||||| | ||||| |||||||| |||||||| || ||  | |||||||||||   |||||||||||||||  |||| ||||| ||||| |||||||
gtagtagatatcctataaaaggattggcacagctatccagttcaactgcataaacatt-tctgctcgttgcagctaattttgccgataatgttttgtgtagCCAAGCTGGCGTAGGCCCAAGGGTATCGACTCCCGCGTCAGGCGGAAGTTCAAGGGATGCACCTTGATGCCCAACATTGGATACGGCTCTGACAAGAAGA

upper sequence: AT5G46430.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S505_19V6.1 (Physcomitrella patens), 3'ss of exon 1
atctatctcattcgtcaaaa----agcttgttttgattctctgatgattatgcttaatcttcattctctgattgttcttttgtttttcaattgttattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA
 |  || |  |   | |       | | ||  |  | |   || || || ||     ||  |||    |||  |  |||| | |    | |  || ||  ||||  || |||||||||||||||||||||||||||  ||||  |  | ||||| |||||    || |||||||||||  | |||||||| ||  | |||||||
-ttgatgttgtggtttagggtttgaacgtgcctgcactacttgttgtttgtgaaatgtca-catctcatgagagaactttgggtgagtattgtttgtt--tcagACAAACTGGAGGAGGCCTAAGGGTATTGACTCTAGGGTTCGCCGCAAGTTTAAGGGCACTACTTTGATGCCCAACATCGGTTACGGCTCAAACAAGAAGA

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|164236138|gb|ES160785.1|ES160785
EST:     GGTCTGCCAAATTCATCAGACCCCAGAGTGATCGCAGAATCACCGTCAAG                         GAAAGACTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTT
genomic: GGTCTGCCAAATTCATCAGACCCCAGAGTGATCGCAGAATCACCGTCAAGgtactcactt ... tattgttcagGAAAG-CTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTT
EST: gi|164119242|gb|ES178816.1|ES178816
EST:     GGTCTGCCAAATTCATCAGACCCCAGAGTGATCGCAGAATCACCGTCAAG                         GAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGG
genomic: GGTCTGCCAAATTCATCAGACCCCAGAGTGATCGCAGAATCACCGTCAAGgtactcactt ... tattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGG
EST: gi|164044228|gb|ES209729.1|ES209729
EST:     TCTGCCAAATTCATCAGACCCCAGAGTTGATCGCAGAATCTACCGTCAAG                         GAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGG
genomic: TCTGCCAAATTCATCAGACCCCAGAGT-GATCGCAGAATC-ACCGTCAAGgtactcactt ... tattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGG
EST: gi|164162786|gb|EL976723.1|EL976723
EST:     GAATCACCGTCAAG                         GAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTC
genomic: GAATCACCGTCAAGgtactcactt ... tattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTC
EST: gi|116422130|gb|EG464722.1|EG464722
EST:     GGTCTGCCAAATTCATCAGACCCCAGAGTGATCGCAGAATCACCGTCAAG                         GAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTC
genomic: GGTCTGCCAAATTCATCAGACCCCAGAGTGATCGCAGAATCACCGTCAAGgtactcactt ... tattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttaatcttcattctctgattgttcttttgtttttcaattgttattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA
                ctctgat  putative branch site (score: 4)
                            ttttgtttttcaattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctatctcattcgtcaaaaagcttgttttgattctctgatgattatgcttaatcttcattctctgattgttcttttgtttttcaattgttattgttcagGAAAGCTGGAGGAGGCCTAAGGGTATTGACTCCCGGGTGAGAAGAAAGTTCAAGGGTGTCACCTTGATGCCCAATGTTGGTTACGGATCTGATAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG