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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttctatggtcattttgtctttaggttacttagaactaggtggttctctacctggttcgtttagccttgttggttcatgtacacagtattgctttc...

Basic information

species Zea mays
transcript GRMZM2G039263_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039263_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 7
GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttc-tatggtcattt-tgt-ctttaggttacttagaactaggtggttctctacctggttcgtttagccttgttggttcatgtacacagtattgctttc
||||| ||||||||||| || || ||||| |||| ||| || || |||||||| |||||  ||||||||||||||||||||||||| |||| | |||||||||| ||| | ||| | | | | || |  |  | ||   || ||     | ||         ||||   ||        || ||     || |      
GTTGATAAACTTGGAAAGGATTCTCTTATAAACTGTGCGAAGACAAGCATGTCCTCGAAGCTGATTAATAGTGACAGTGATTTCTTCGCAAATCTGgtaagttcctattgccatatatatacatttgtattttcagctgtaagtttgattttagtgatactttttaaatttaaataaatatttagttgatactcta---
















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|211250617|gb|FL215180.1|FL215180
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGT-AAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|149010855|gb|EE042239.2|EE042239
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|211239408|gb|FL328610.1|FL328610
EST:     TCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: TCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|33104341|gb|CF064301.1|CF064301
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|211250619|gb|FL215182.1|FL215182
EST:     ATGTCTTCGAAATTGATTAATAGTGACAGTGGATT-CTTTGCCACCTTTG                         GTTGGTGAGGCAGTTCAAG
genomic: ATGTCTTCGAAATTGATTAATAGTGACAGTG-ATTTCTTTGCAAC-TTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAG
EST: gi|211149768|gb|FL359580.1|FL359580
EST:     TAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: TAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|211248391|gb|FL215168.1|FL215168
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAAGCAGTTCAAGCCGTGAAGACTACAA-TGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|19058770|gb|BM737437.1|BM737437
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|211378069|gb|FL215200.1|FL215200
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|149083358|gb|EE172656.2|EE172656
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|149074901|gb|EE163349.2|EE163349
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCA
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCA
EST: gi|211383347|gb|FL215220.1|FL215220
EST:     CATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTTGCA-CTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAG
genomic: CATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTT-GCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAG
EST: gi|149000083|gb|EE037198.2|EE037198
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|60396669|gb|DN229537.1|DN229537
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|67021395|gb|CO450144.1|CO450144
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|33092579|gb|CF052573.1|CF052573
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGCGAAGACTGCAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|211243912|gb|FL215132.1|FL215132
EST:     GCATGTCTTCGAAATTGATTAATAGGGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGNTCAAGCCGTGAAAACTACAA
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAA
EST: gi|71437844|gb|DR818894.1|DR818894
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|211195400|gb|FL324707.1|FL324707
EST:     TCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: TCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|211383348|gb|FL215221.1|FL215221
EST:     ATGTCTTCGAAATTTGAT-AATAGTGACAGTGATTTCTTTGCAAACTTTG                         GTTGT-GAGGCAGTTCAAGCCGTGAAGACTACAA-TGCCAAG
genomic: ATGTCTTCGAAATT-GATTAATAGTGACAGTGATTTCTTTGCAA-CTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAG
EST: gi|33102590|gb|CF062550.1|CF062550
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|22490780|gb|BU050703.1|BU050703
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
EST: gi|61119168|gb|DN560129.1|DN560129
EST:     GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTG                         GTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG
genomic: GCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTG

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: 678

GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTGAAATATCCAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTGAAATATCCAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTGAAATATCCAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

GTTGACAAACTTGGAAAAGAATCCCTTATCAACTCTGCAAAAACTAGCATGTCTTCGAAATTGATTAATAGTGACAGTGATTTCTTTGCAACTTTGgtaagttcta ... gatttcttagGTTGTTGAGGCAGTTCAAGCCGTGAAGACTACAAATGCCAAGGGAGACGTGAAATATCCAATCAAG