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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagatacaatacaacatacacccttccttaatatactgtcacttttcaagtgttttgagtattcaatgtccactagaagatgtgctcaactagatttacttctttttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAA

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 16
gtcagatacaatacaacatacacccttccttaatatactgtcacttttcaagtgttttgagtattcaatgtc--cactagaagatgtgctcaactagatttacttctttttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAA
|| || | | |||||   | |||  |||      |   ||   ||||||  |   ||  | ||   ||| ||  |||     | | | |||||  || ||| || ||    | || ||||||||||| |||||||||||| ||||| | ||||||||| ||||||| ||||||||||||||||| ||||| ||||| ||||||| |   ||||||||||
gttagtt-cgatacacgctccacatttctaccgcactatgctgcttttcttgaacttcta-tacagaatttccccacacatggctatactcaatgaggttttctgct----gatatcagGCCACAGAAATTTGGAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAA
















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|22491259|gb|BU051182.1|BU051182
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|33102735|gb|CF062695.1|CF062695
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|211465903|gb|FL134195.1|FL134195
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGAAATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|78021086|gb|DV489473.1|DV489473
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|148970819|gb|EE021583.2|EE021583
EST:     GGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: GGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|211465904|gb|FL134196.1|FL134196
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGAAATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|32943853|gb|CF048672.1|CF048672
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|15499663|gb|BI596176.1|BI596176
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGGTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|32832265|gb|CD971943.1|CD971943
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|67026638|gb|CO455387.1|CO455387
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|12968725|gb|BG265671.1|BG265671
EST:     AGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: AGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|31351811|gb|CD436168.1|CD436168
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGAAATTTGGAACATCATCTCAAATGGGGGTTACTTATAT
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATAT
EST: gi|60357924|gb|DN224897.1|DN224897
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|37376046|gb|CF624519.1|CF624519
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|15632677|gb|BI679770.1|BI679770
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|211465906|gb|FL134198.1|FL134198
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGAAATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|32835080|gb|CD974758.1|CD974758
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|67033233|gb|CO461982.1|CO461982
EST:     CTCGGGAGGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGAAATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|19437266|gb|BM953676.1|BM953676
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|37388048|gb|CF631228.1|CF631228
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
EST: gi|32835719|gb|CD975397.1|CD975397
EST:     CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAG                         GCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC
genomic: CTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGC

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), 48 (downstream exon)
Score: 247

GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 439

GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 508

GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 480

GCAAACTTTCCTTGAGGAGGGGGCGCTTTCTGAGCTAATTGTTGCATTCTCTCGGGAAGGGCCAACGAAAGAATATGTGCAGCATAAGATGGTGGAAAAGgtcagataca ... ttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaatgtccactagaagatgtgctcaactagatttacttctttttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAA
                                  tttacttctttttgtt  CT-rich tract
                                 atttacttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagatacaatacaacatacacccttccttaatatactgtcacttttcaagtgttttgagtattcaatgtccactagaagatgtgctcaactagatttacttctttttgttaccagGCCACAGATATTTGGAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG