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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaactgtatttctgttatgcaaataatagaaatgggggtatccttcctctcagcgagcataatctatttgctgtgatgatgtatatactttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT

Basic information

species Zea mays
transcript GRMZM2G125556_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125556_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 1
cttaactgtatttctgttatgcaaataatagaaatgggggtatccttcctctcagcgagcataatctatttgctgtgatgatgtatatactttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT
||| || || || | | || | | | | | || || || | | | | | |||||| | ||||||||| |||| |||||||| ||||| ||||| | ||||||||||| ||| |||||| | | ||||| |||||||||||||| ||||||||
attagaaactgttgtgggatcagtgtctctttagtgaattagtgtggatttttgtttgctacggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT
















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|211475755|gb|FL124812.1|FL124812
EST:     GGAAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|76285485|gb|DV025053.1|DV025053
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211041272|gb|FL124819.1|FL124819
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211464236|gb|FL298400.1|FL298400
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211041270|gb|FL124817.1|FL124817
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211041278|gb|FL124825.1|FL124825
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211464240|gb|FL298404.1|FL298404
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211041276|gb|FL124823.1|FL124823
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA--                         ---C-GAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211464238|gb|FL298402.1|FL298402
EST:     -GGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211466770|gb|FL298415.1|FL298415
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211041277|gb|FL124824.1|FL124824
EST:     GGNAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAA--                         ---C-GAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211041274|gb|FL124821.1|FL124821
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211475759|gb|FL124816.1|FL124816
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211475756|gb|FL124813.1|FL124813
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211041273|gb|FL124820.1|FL124820
EST:     GG-AAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211041271|gb|FL124818.1|FL124818
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211475757|gb|FL124814.1|FL124814
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|93282356|gb|EB674620.1|EB674620
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211466771|gb|FL298416.1|FL298416
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
EST: gi|211464237|gb|FL298401.1|FL298401
EST:     GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACG                         GTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC
genomic: GGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGC

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: 369

TGTCCTCGCCGACAGGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 751

TGTCCTCGCCGACAGGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 879

TGTCCTCGCCGACAGGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 547

TGTCCTCGCCGACAGGGAAAGCCGTGTTGCAAGAAGGGGAATTCCGCTGCGAGATCCGTGAACGgtcagttcgc ... tttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctctcagcgagcataatctatttgctgtgatgatgtatatactttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT
                                          tactttctt  CT-rich tract
 ataatctattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaactgtatttctgttatgcaaataatagaaatgggggtatccttcctctcagcgagcataatctatttgctgtgatgatgtatatactttcttgcagGTTCAGAGATGGCACAGACGGTGTTCACCCCCTCTTTGGAAGCGATGAAGCATGTCAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT

- - - tgtattt
- - - - - - - - ttatgca
- - - - - - - - - - - - - aatagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat