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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttggttcattttcaattaaagcaagccattttagatttagagcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG

Basic information

species Zea mays
transcript GRMZM2G115424_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
---tcttggttcattttcaattaaagcaagccattttagatttagagcctgaaac---aaccgcaa-ataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG
    |||  |    |  ||| ||     | ||     ||| | |     ||||     |   ||||  |   |||||   || ||||| || || |  ||   | ||||||||| ||||| ||| |||||||  |||| ||||| ||||||||||| || ||||||| |||||| || ||||||||||| || ||||||||  | ||
tgtccttcataatctcccaaataggaagaacc-caagagaatgattttttgaagtgttatttgcaatgtgttttatt---aacattatgttattctcgtt---gtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG

upper sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G00630.1 (Glycine max), 3'ss of exon 2
---tcttggttcattttcaattaaagcaagccattttagatttagagcctgaaac---aaccgcaa-ataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG
    |||  |    |  ||| ||     | ||     ||| | |     ||||     |   ||||  |   || ||   || ||||| || || |  ||   | ||||||||| ||||| ||| |||||||  |||| ||||| ||||||||||| || ||||||| |||||| || ||||||||||| || ||||||||  | ||
tgtccttcataatctcccaaataggaagaacc-caaaagaatgattttttgaagtgttatttgcaatgtgttttgtt---aacattatgttattctcgtt---gtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG

upper sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------------------------------------tcttg-gttcattttcaattaaagcaagccatttta-gatttagagcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG
                                                                               | ||| | |  | |    || ||    |    || | |||| ||    | |  |  || |       || |||   |   | |||  || |  |||  | ||||||||| ||||| ||| | ||||||||||| |||||||||||||| || ||  | || | |||||| ||||||||||| || || || |||||| | ||
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG

upper sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
-tcttggttcattttcaattaaagcaagccattttagatttagagcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG
 | ||      |||   |     | |  | |   |  | ||||  |            |   |      |||  | |    |    ||||   |   ||||||||||| || || ||| | ||||||||||| |||||||||||||| || ||  | || | ||||||||| |||||||| || || || |||||  | ||
ctttttaagtgtttgtgagatttgtac-ctaagatgaagttagttctctttgtggtttctcttcttgacttcttagtgaattacgttttttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG

upper sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
tcttggttcattttcaattaaagca--agccattttagatttaga--gcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG
  ||  || || |||| ||    ||  | |||| |     |||    | |  |||  |  |||| |  ||||||    || || | |   |||||| |    ||||||||| || || ||| | ||||||||||| ||||||||||||||||| ||| |||||| ||||||||| |||||||| || ||||| |||||  | ||
--ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtt-tgtaaatttgttct-tatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG

upper sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S38_137V6.1 (Physcomitrella patens), 3'ss of exon 3
tcttggttcattttcaattaaagcaagccattttagattt-agagcctgaaaca-accgcaa-ataccttattcgaaatattattt-tcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG
  ||||    |    ||   |  ||     | || ||    |||  | ||  ||   || |   |   | |    |  ||    |  |||  ||  ||||  ||||||||| ||||| ||| | || ||  | ||  ||||| ||||||||||||| || || || || ||||||||||||||||| ||||| || || || ||
-attggagggtacataag-gatccagtttgtattggaagagagattcggaggcatgtcgtagcgtgtatcacatcacgtagcggtggtctgctgaattgc--agAGAAGGAGAATTTGTGTCTGTACGGTTTCCCGGATGAGGCATGGGAAGTAAATTTACCAGCAGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCCCTTGG

upper sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2
-----tcttggttcattttcaattaaagcaagccattttagatttagagcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG
       | ||   ||||| |  ||      ||||| |  | |  |   | |    |      |  |      ||  ||||  | |||  ||||       ||||||||||| ||||| || ||||||||  ||||  | ||  |||||||||||||  | || ||||| ||||||||||||||||| ||||| || ||||| ||
gttttcgtagggcaattttgaggtagttggtgccatgt--gttacatcacttagcgctttgttatgtga---gttttaaatgatttttatttttccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG

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|18384050|gb|BM417250.1|BM417250
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         AGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAA
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAA
EST: gi|76018651|gb|DT945821.1|DT945821
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         AGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
EST: gi|17969981|gb|BM276750.1|BM276750
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         AGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
EST: gi|17970075|gb|BM276842.1|BM276842
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         AGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
EST: gi|19821822|gb|BQ047846.1|BQ047846
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         AGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
EST: gi|37418399|gb|CF646868.1|CF646868
EST:     CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         AGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
EST: gi|18964760|gb|BM661194.1|BM661194
EST:     CGGGACTACCTGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCG                         AGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
genomic: CGGGACTACC-GCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
EST: gi|31353558|gb|CD437915.1|CD437915
EST:     CCGGGACTACCGCGCGCGCCAGGACGGCCTAATCAGGGCGCTCACCACCG                         AGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA
genomic: CCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAA

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: 46 (upstream exon), 49 (downstream exon)
Score: 212

GGAGCCGGCTTCCCTGGCACGCCGGTCCCGCGCTCGCCGGAGGACGTTTTCCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 146

GGAGCCGGCTTCCCTGGCACGCCGGTCCCGCGCTCGCCGGAGGACGTTTTCCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 164

GGAGCCGGCTTCCCTGGCACGCCGGTCCCGCGCTCGCCGGAGGACGTTTTCCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 58

GGAGCCGGCTTCCCTGGCACGCCGGTCCCGCGCTCGCCGGAGGACGTTTTCCGGGACTACCGCGCGCGCCAGGCCGGCCTAATCAGGGCGCTCACCACCGgtaatgcccg ... ttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG
                                ttattttcttttgttt  CT-rich tract
                    ttattcgaaatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttggttcattttcaattaaagcaagccattttagatttagagcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - ttcattt
- - - - - - - - - - - gcaagcc
- - - - - - - - - - - - - - - - - - - - - -gcctgaa