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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctagtattctagtttcaacattaacatatttatgaacttcaaagtgaagcaacgaatcacagcattcattcactaataaccacttcttttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC

Basic information

species Zea mays
transcript GRMZM2G064023_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 5
atctagtattctagtttcaacattaacata-tttatgaacttcaaa-gtgaagcaacgaatcacagcattcattcactaataaccacttcttttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC
 | | |  ||  ||||  ||| |      | ||| |||| || ||| ||| | ||    ||        |  |  |   | | |    ||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||| |||| ||||| ||||||||||| |||||||||||||||||||
-ttttgagttagagttgtaacttagttggaatttgtgaaatttaaacgtgtatcactccat-gttttgctgttggatgtaaatctctctcttttctatccagGGTATTCGTTTCAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCAACAGCAATTAAAGGTGGAGAACCTTTGCCGGAGGGTCTCCTTTGGCTTC

upper sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 6
---atctagtattctagtttcaacattaacatatttatgaacttcaaa-gtgaagcaacgaatcaca-gcattcattcactaataaccacttcttttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC
   |  |||  || ||| ||  |  || ||   ||| |||| || ||| ||| | ||    ||  |  ||  |        | |    || ||||| |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| | ||| || ||||||||||||||||| ||||||||||
ttaagttagatttttagctt--agtttgac---tttgtgaaatttaaacgtgcatcactctatatcttgctgttggatgtaagtctgtacctctttcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTC
















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|211269895|gb|FL099815.1|FL099815
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211399063|gb|FL099822.1|FL099822
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|8103179|gb|AW927835.1|AW927835
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|76287895|gb|DV027463.1|DV027463
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|4609628|gb|AI600467.1|AI600467
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|149082725|gb|EE171943.2|EE171943
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211269899|gb|FL099819.1|FL099819
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211269892|gb|FL099812.1|FL099812
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGANGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|71450120|gb|DR831170.1|DR831170
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211269897|gb|FL099817.1|FL099817
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211269890|gb|FL099810.1|FL099810
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211399064|gb|FL099823.1|FL099823
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|213174510|gb|FM184748.1|FM184748
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211399065|gb|FL099824.1|FL099824
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAA
EST: gi|211269891|gb|FL099811.1|FL099811
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTG
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTG
EST: gi|211269901|gb|FL099821.1|FL099821
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211269900|gb|FL099820.1|FL099820
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCYAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAA
EST: gi|211269898|gb|FL099818.1|FL099818
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGC-A
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|149077813|gb|EE166538.2|EE166538
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|211269893|gb|FL099813.1|FL099813
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|32859373|gb|CD999054.1|CD999054
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
EST: gi|149090362|gb|EE179668.2|EE179668
EST:     GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA
genomic: GAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgc ... ttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagcaacgaatcacagcattcattcactaataaccacttcttttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC
                              taataac  putative branch site (score: 1)
                                    ccacttcttttctatc  CT-rich tract
                            actaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctagtattctagtttcaacattaacatatttatgaacttcaaagtgaagcaacgaatcacagcattcattcactaataaccacttcttttctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGTGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - -caacgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattca