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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTGGCACCAAAGTTATACCACATGAAGATTGCATTGGGACATTACAAGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaatgtcagaaaaaccgagctagtcctttcgatgttattctgaacaaccacattcttttttggatttattttcattcggttaaaccaactgcaccataatgatttacag

Basic information

species Arabidopsis thaliana
transcript AT5G16710.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G16710.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM5G826194_T02 (Zea mays), 5'ss of exon 5
GTCCTTGGCACCAAAGTTATACCACATGAAGATTGCATTGGGACATTACAAGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaata--aatgtcagaaaaaccgagctagtcctttcgatgttattctgaacaaccacattcttttttggatttattttcattcggttaaaccaactgcaccataatgatttacag
 ||  |||  || ||  |||| |||||| ||||  |  |||| || |||||||| ||||||||||||||||||||| |||  || ||| | || ||| |||||  ||   |||||  | | |  ||     || ||  | |  | || |    ||  |  || | ||   |    |   |      ||       | ||||| |||||| ||     
CTCTCTGGGTCCTAAACTATATCACATGGAGATAACTCTGGGCCACTACAAGAATTGGTCTGTTCCAGATTCACTTTCTTATGTAAAAACATATATGAAGgtatgtatccatgtcctacacaatga-----tctttgagcttatctttttggtaattagtttttattggaggaagaaggttccatagt-------attgcac-ataatgtttg----

upper sequence: AT5G16710.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv14s0006g00630.t01 (Vitis vinifera), 5'ss of exon 5
GTCCTTGGCACCAAAGTTATACCACATGAAGATTGCATTGGGACATTACAAGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaat--aaatgtcagaaaaaccgagctagtcctttcgatgttattctgaacaaccacattcttttttggatttattttcattcggttaaaccaactgcaccataatgatttacag
|||  | | ||||||  |||||||  |  ||||||| ||||| ||||||||||| ||| | ||||||||||| ||||| || || || || |||||| |||||  |  | | | || | | |   || |  || | | | |||     |||  | | | |||         ||  |   |   ||   |      | |  |  | |           
GTCTCTTGGACCAAAACTATACCATCTAGAGATTGCTTTGGGGCATTACAAGAAGTGGACGGTTCCAGATTCTCTTCCCTTTGTGAAGTCTTACATGAAGgtatgtctacaagccaaacatatt-agatgttcatcttgctgta----tgagta-ctatatttagcagcatatggaaaatatctcaactgtgttgaatatagaaaa-----------
















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|19799493|gb|AU230783.1|AU230783
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGA-CACACGGCCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|125228838|gb|EL242923.1|EL242923
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|116480640|gb|EG523232.1|EG523232
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|86076765|gb|DR372522.1|DR372522
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|124940042|gb|EL016531.1|EL016531
EST:     TCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: TCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|125290000|gb|EL304085.1|EL304085
EST:     ACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: ACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|116480635|gb|EG523227.1|EG523227
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|116480632|gb|EG523224.1|EG523224
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|116480636|gb|EG523228.1|EG523228
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|116480645|gb|EG523237.1|EG523237
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|116480622|gb|EG523214.1|EG523214
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|124932039|gb|EL009339.1|EL009339
EST:     TCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: TCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|116480638|gb|EG523230.1|EG523230
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|125069949|gb|EL135542.1|EL135542
EST:     TTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: TTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|116480643|gb|EG523235.1|EG523235
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
EST: gi|116480631|gb|EG523223.1|EG523223
EST:     AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAG                         AATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT
genomic: AGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaat ... tgatttacagAATGTTTTCTCGAGGGAATCATTCACGAACACACGGGCGGAAACAGAGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTTGGCACCAAAGTTATACCACATGAAGATTGCATTGGGACATTACAAGAACTGGTCTGTTCCAGATTCACTTCCTTTCGTCAAATCCTACATGGAGgtaaataaatgtcagaaaaaccgagctagtcctttcgatgttattctgaacaaccacattcttttttggatttattttcattcggttaaaccaactgcaccataatgatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA