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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgttttatgtgacttgattttttacgcgcattatgctatgaacaaaatttctttttctgcggttaaatcaaaggataaaataactcattttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATTTCCAAGAAGTTGCCTCCAAAGCTGTATTTTGCTGTTAACAAGCCAAAGG

Basic information

species Zea mays
transcript GRMZM2G315806_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315806_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g05806.1 (Oryza sativa), 3'ss of exon 2
---aactgttttatgtgacttgattttt-tacgcgcattatgct-atgaacaaaatttctttttctgcggttaaatcaaaggataaaataactcattttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATTTCCAAGAAGTTGCCTCCAAAGCTGTATTTTGCTGTTAACAAGCCAAAGG
    | | |  ||||    |||||   | | |    | | |  | ||  ||||  ||  | |||     |||| ||   |   | | | |     |||| || |||||||||||||||||||||||||||||||||| ||||| || |||||||||||||||||| | ||||| ||| | ||||||||||||||||||||||| |
ggtcattttactatgaattttgatccatgtgcttcaaatgtattcatagacaagtttattattt-----gttacatatgattcttatacattcttttttatgtagACCAAAGTTGACATCTCAAAGGATTCTATCTATGTTAATGGAAACCGCATTTCCAAGAAGCTTCCTCCGAAGTTATATTTTGCTGTTAACAAGCCAAAAG
















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|148987677|gb|EE031557.2|EE031557
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|148957814|gb|EC903956.2|EC903956
EST:     TTCCAAGGGAAGGTGGACTGTCAATGGTTCAGTCTGTACTTCTCCCTCAA                         ACCAAAGT-GA-ACTCTCAAAGGATTCTATCTACGTTAACGGGAACCGCA
genomic: TTCCAAGGGAAGGTG-ACTGTCAATGGTTCAGTCTGTACTTCTCC-TCAGgtattaattc ... ttttgtgcagACCAAAGTTGACA-TCTCAAAGGATTCTATCTACGTTAACGGGAACCGCA
EST: gi|78111429|gb|DV529826.1|DV529826
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|71310508|gb|DR791549.1|DR791549
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|50330874|gb|CO526000.1|CO526000
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|149079210|gb|EE168172.2|EE168172
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|149083253|gb|EE172532.2|EE172532
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|211519990|gb|FL114312.1|FL114312
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCCAAAGT-GACATCTCAAA
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACC-AAAGTTGACATCTCAAA
EST: gi|211519996|gb|FL114318.1|FL114318
EST:     CTTCCAAGGGAAGGTGACTGGNCA-TGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCA
genomic: CTTCCAAGGGAAGGTGACTGT-CAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCA
EST: gi|74237372|gb|DT645286.1|DT645286
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|89761484|gb|DY689481.1|DY689481
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAA
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAA
EST: gi|71446099|gb|DR827149.1|DR827149
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|148946321|gb|EC891627.2|EC891627
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|50331088|gb|CO526214.1|CO526214
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|14191222|gb|BG833452.1|BG833452
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAATCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCACATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|148938500|gb|EC882821.2|EC882821
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|71436711|gb|DR817761.1|DR817761
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|101386864|gb|EB815449.1|EB815449
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|14191223|gb|BG833453.1|BG833453
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAATCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCACATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
EST: gi|71306649|gb|DR789484.1|DR789484
EST:     TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAG                         ACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT
genomic: TCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATT

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: 48 (upstream exon), 45 (downstream exon)
Score: 34

TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATTTCCAAGAAGTTGCCTCCAAAGCTGTATTTTGCTGTTAACAAGCCAAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATTTCCAAGAAGTTGCCTCCAAAGCTGTATTTTGCTGTTAACAAGCCAAAGG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 22

TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATTTCCAAGAAGTTGCCTCCAAAGCTGTATTTTGCTGTTAACAAGCCAAAGG


Block sizes: 43 (upstream exon), 44 (downstream exon)
Score: 27

TGGCATCAAGAAGGACCAGTGAGGAGCTCATCTTCCAAGGGAAGGTGACTGTCAATGGTTCAGTCTGTACTTCTCCTCAGgtattaattc ... ttttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATTTCCAAGAAGTTGCCTCCAAAGCTGTATTTTGCTGTTAACAAGCCAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaatttctttttctgcggttaaatcaaaggataaaataactcattttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATTTCCAAGAAGTTGCCTCCAAAGCTGTATTTTGCTGTTAACAAGCCAAAGG
                                   aaataac  putative branch site (score: 27)
                                         ctcatttt  CT-rich tract
                    ttaaatcaaaggataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgttttatgtgacttgattttttacgcgcattatgctatgaacaaaatttctttttctgcggttaaatcaaaggataaaataactcattttgtgcagACCAAAGTTGACATCTCAAAGGATTCTATCTACGTTAACGGGAACCGCATTTCCAAGAAGTTGCCTCCAAAGCTGTATTTTGCTGTTAACAAGCCAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
-actgttt
- - - - - - - - - - - - - - - - - - tgctatg
- - - - - - - - - - - - - - - - - - - - - -aacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa