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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattccttgcattcacagtatttacaaagtccttacctcacacatggttatacattgaatattgtaaaatgcaggaatctggtttaacttcaatc...

Basic information

species Zea mays
transcript GRMZM2G100620_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100620_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g15700.1 (Oryza sativa), 5'ss of exon 3
TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattccttgcattcacagtatttacaaagtc---cttacctcacacatggttatacat-tgaatattgtaaaatgcagga--atctggtttaacttcaatc
|||||||||| ||||| |||||| | || || || || ||||||||||| | |||||||||||| ||||| |||||||||||| ||| |||| || ||| |  ||    | |     |||  ||| ||||| || ||||| | |||||||| || | ||| |  |  | ||| |  |      
TTAAGATTGGAAGACCTGGGTATCAGGTGACTAAGCAGTATGATCCTGACATGAAGCAACACTCATTTCTTTTTGAGgtcagtgttcattgcgtttacatttgtttggcacttgaatttaattcatacatgtttttacatgttaatattgtgaagtccagaacaaattagttcactt------
















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|211397253|gb|FL247604.1|FL247604
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|19351244|gb|BM895776.1|BM895776
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|149014483|gb|EE044106.2|EE044106
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|19272503|gb|BM888759.1|BM888759
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|211397250|gb|FL247601.1|FL247601
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|211458287|gb|FL247622.1|FL247622
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|149111001|gb|EE294500.2|EE294500
EST:     ATATGATCTTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCTTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: ATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|91056062|gb|EB166480.1|EB166480
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|18648819|gb|BM497638.1|BM497638
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|148944813|gb|EC889958.2|EC889958
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|78092801|gb|DV521175.1|DV521175
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|211460800|gb|FL247626.1|FL247626
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCA
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCA
EST: gi|78077143|gb|DV505577.1|DV505577
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|148937013|gb|EC881184.2|EC881184
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|71439882|gb|DR820932.1|DR820932
EST:     CGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: CGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|149111002|gb|EE294501.2|EE294501
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|37417746|gb|CF646533.1|CF646533
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|50330974|gb|CO526100.1|CO526100
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|78113433|gb|DV531825.1|DV531825
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|32863198|gb|CF002880.1|CF002880
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|6564142|gb|AW231764.1|AW231764
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|149081122|gb|EE170228.2|EE170228
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|211458278|gb|FL247613.1|FL247613
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGC
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGC
EST: gi|211402594|gb|FL136251.1|FL136251
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|211402593|gb|FL136250.1|FL136250
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGAT
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGAT
EST: gi|32803496|gb|CD955732.1|CD955732
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
EST: gi|211460801|gb|FL247627.1|FL247627
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACGCTGAA
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAA
EST: gi|18648881|gb|BM497700.1|BM497700
EST:     TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAG                         ATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG
genomic: TAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 188

TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattc ... ttcattttagATTGGTTACCCTGAAATTGAAGATAATTGCAAGCCAAGGCACCGCTTCATGTCATCATATGAACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAAGATTGGCAGACCCGGGTATAAAGTAACCAAACAATATGATCCTGAGACGAAGCAACACTCGTTTCTCTTTGAGgtcagtattccttgcattcacagtatttacaaagtccttacctcacacatggttatacattgaatattgtaaaatgcaggaatctggtttaacttcaatc

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA