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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCAGATATTCGTCTCGTGTGCAAAGAAGCTGCCATGCAACCACTGAGACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaattttttggttcttttgtgatttttgttggaattttcttttatgtatccagttaatttgtaccatgttagtttaaaaacacaaaatataggtccttgagttacgcgtactattatccgcaggcccaatgaacatatcttacatttctgtgttttttacgggtttgcag

Basic information

species Zea mays
transcript GRMZM2G022777_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022777_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g55260.2 (Oryza sativa), 5'ss of exon 9
GGTTCAGATATTCGTCTCGTGTGCAAAGAAGCTGCCATGCAACCACTGAGACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaattttttggttcttttgtgatttttgttggaattttcttttatgtatccagttaatttgtaccatgttagtttaaaaacacaaaatataggtccttgagttacgcgtactattatccgcaggcccaatgaacatatcttacatttctgtgttttttacgggtttgcag
||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||| |||||||||||||||||||| || ||| |||| || ||||||||| | |||| ||||||||| | | |  || |   ||||| |||| ||       | || || |||||  | |  | |||||    ||||  | |   |||  |||| | |  | ||||  | |  ||         | ||||   || | |                    
GGTTCAGATATCCGTCTTGTGTGCAAAGAAGCTGCCATGCAACCACTAAGACGTCTTATGTCAGTTCTTGAAGCCAGAGATGAGCTGGTGCCTGAGGAAGgttagtttt-ggttcttttctcagtgatgct---atttttttttctg------atgaaattataccac-tgaactgaaaaa----aaattcatgctattg--ttacacat--ttttatgtg-atacct------tttctcttgggttgcag--------------------
















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|149046686|gb|EE048076.2|EE048076
EST:     AGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: AGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|60401221|gb|DN234028.1|DN234028
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|60336952|gb|DN203925.1|DN203925
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|149035100|gb|EE155086.2|EE155086
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|60356145|gb|DN223118.1|DN223118
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|7216903|gb|AW563025.1|AW563025
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|76934720|gb|DV173991.1|DV173991
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|87152206|gb|DY396995.1|DY396995
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|30704808|gb|CD058607.1|CD058607
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|24770082|gb|CA405211.1|CA405211
EST:     CAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAACCCTGATGATATTGAACTTGCATTAA
genomic: CAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|7137663|gb|AW499208.1|AW499208
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCA
EST: gi|76933169|gb|DV173348.1|DV173348
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|78109694|gb|DV528110.1|DV528110
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|71447792|gb|DR828842.1|DR828842
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAATCCTGATGATATTGAACTTGCATTA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAA-CCTGATGATATTGAACTTGCATTA
EST: gi|67012372|gb|CO441121.1|CO441121
EST:     ACGTCTCATGTCTGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AATTGCCTGAGGTTGGTCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|4827733|gb|AI668425.1|AI668425
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|9733829|gb|BE512581.1|BE512581
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|76280582|gb|DV020150.1|DV020150
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|78023793|gb|DV492180.1|DV492180
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|71447793|gb|DR828843.1|DR828843
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|148963078|gb|EE014035.2|EE014035
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|60345869|gb|DN212842.1|DN212842
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|76281418|gb|DV020986.1|DV020986
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|91051055|gb|EB161473.1|EB161473
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|22490578|gb|BU050501.1|BU050501
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|40336431|gb|CK370501.1|CK370501
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
EST: gi|32836835|gb|CD976513.1|CD976513
EST:     ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAG                         AACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA
genomic: ACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAA

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: 274

GGTTCAGATATTCGTCTCGTGTGCAAAGAAGCTGCCATGCAACCACTGAGACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAAGGAACACTAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GGTTCAGATATTCGTCTCGTGTGCAAAGAAGCTGCCATGCAACCACTGAGACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAAGGAACACTAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 209

GGTTCAGATATTCGTCTCGTGTGCAAAGAAGCTGCCATGCAACCACTGAGACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAAGGAACACTAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

GGTTCAGATATTCGTCTCGTGTGCAAAGAAGCTGCCATGCAACCACTGAGACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaatttttt ... gggtttgcagAACTGCCTGAGGTTGGCCCTCTGAAACCTGATGATATTGAACTTGCATTAAGGAACACTAGGCCGTCAGCACATCTCCATGCGCATCGCTATGAGAAGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTCAGATATTCGTCTCGTGTGCAAAGAAGCTGCCATGCAACCACTGAGACGTCTCATGTCAGTTCTTGAAGCCAGTGACGAGTTGGTTCCGGAGGAAGgtaattttttggttcttttgtgatttttgttggaattttcttttatgtatccagttaatttgtaccatgttagtttaaaaacacaaaatataggtccttgagttacgcgtactattatccgcaggcccaatgaacatatcttacatttctgtgttttttacgggtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA