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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtactttttccataccaattttaagcaagttttctgtaagaggaacaaattcaattttatggtaattgattttccattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA

Basic information

species Zea mays
transcript GRMZM2G039263_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 12
gtttgtactttttccataccaattttaagcaagttttctgta-agaggaacaaattcaattttatggtaat------tgattttccattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA
|| ||||||||| | || || ||   || |   | || |||| |    ||| |     | |||| || |||      ||  ||||  || |||||||||| || |||||||| ||||||||||||| |||||| |||||||||||  | || |||||||||||  ||||||||||||||||||| |||||||| |
gtatgtactttt-caattcccatgcaaatcttatattttgtataaccaaaccagcaagagtttaggggaatcacgcctgcatttcttttatgcagGTCTCAATTATACTTAGAGGCGCAAATGACTTCATGCTAGATGAGATTGACAGATCATTGCATGATGCATTGTGCATTGTGAAGAGAACTCTGGAATCCA

upper sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------------------------------------------gtttgtactttttccataccaattttaagcaagttttctgtaagaggaacaaattcaa-------ttttatg---gtaattgattttccattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA
                                                             |  |  ||    |||    ||||||    ||||    ||  |   | |  ||          ||| |||    ||| || ||||    |||  |||||||  | ||  | || || |||||||||||||||||||||||||| ||  |  |  ||||||| ||  | || ||||| ||||| ||||| || || |
gtatgccattctctcagcaatgaatcttacttgattgctgacagtactatatcacacaaaatcaatcttaagtatatttcttttaaagttgtttaacatatcacacagagttttgtctaggtttttcatgtttataagtgtttttttcctgt-tagGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAGAGAGCACTGCATGACGCTTTATGTATTGTCAAGAGGACCCTTGAGTCCA
















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|32944569|gb|CF049388.1|CF049388
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|211163739|gb|FL337964.1|FL337964
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|211469892|gb|FL096481.1|FL096481
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32929201|gb|CF034013.1|CF034013
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32928649|gb|CF033461.1|CF033461
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|22935598|gb|BU571873.1|BU571873
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|21389952|gb|BQ528001.1|BQ528001
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|22521580|gb|BU080391.1|BU080391
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|67015007|gb|CO443756.1|CO443756
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32806379|gb|CD958613.1|CD958613
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|33094774|gb|CF054768.1|CF054768
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|37400207|gb|CF637451.1|CF637451
EST:     AAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: AAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32937857|gb|CF042676.1|CF042676
EST:     GTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: GTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32929620|gb|CF034432.1|CF034432
EST:     TTACTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32806779|gb|CD959013.1|CD959013
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCATCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32928302|gb|CF033114.1|CF033114
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32938970|gb|CF043789.1|CF043789
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|24934261|gb|CA452479.1|CA452479
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|166665607|gb|EG258903.1|EG258903
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGC
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGC
EST: gi|32808822|gb|CD961056.1|CD961056
EST:     TTGCTGACGATGATGTTATCCTGGAGAAAGGCACAAAGAGCACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32938969|gb|CF043788.1|CF043788
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGGCTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|211469893|gb|FL096482.1|FL096482
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|60350871|gb|DN217844.1|DN217844
EST:     GTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: GTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|67021395|gb|CO450144.1|CO450144
EST:     GCTGACGATGATNGT-ATTCTGGTGAAAAGGCACAA-GA-CACCANCGCG                         GTCTCTATA-TACTTAGGGGCGCAA-TGACTACATGCT-GATGAGA
genomic: GCTGACGATGAT-GTTATTCTGGTGAAA-GGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGA
EST: gi|26559466|gb|CA831701.1|CA831701
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32937830|gb|CF042649.1|CF042649
EST:     GTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: GTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|60343155|gb|DN210128.1|DN210128
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|84977527|gb|DW475949.1|DW475949
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|32939416|gb|CF044235.1|CF044235
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|61119168|gb|DN560129.1|DN560129
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTANGGGCGCAAATGACTACATGC
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGC
EST: gi|67018449|gb|CO447198.1|CO447198
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
EST: gi|87157304|gb|DY402093.1|DY402093
EST:     TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCG                         GTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA
genomic: TTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAA

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: 487

ATTCGATTCATCATTCCTTGGCCATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 190

ATTCGATTCATCATTCCTTGGCCATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

ATTCGATTCATCATTCCTTGGCCATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 135

ATTCGATTCATCATTCCTTGGCCATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGACGATGATGTTATTCTGGTGAAAGGCACAAAGAACACCAGCGCGgtttgtactt ... cattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgtaagaggaacaaattcaattttatggtaattgattttccattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA
                                  aattgat  putative branch site (score: 135)
                                        ttttccatt  CT-rich tract
                 aaattcaattttatgg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtactttttccataccaattttaagcaagttttctgtaagaggaacaaattcaattttatggtaattgattttccattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA