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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataccaaatcttgactttcataatcaacacagttgttatatatcggtgcatgtctacaaacatgtaaaaacataagaagtattttgcctatgcactagaaaggcaaaacactaggatccaaacttcccgaagactccataccttatcacggtttctaccatgttatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCGAAGAATCCCTCCGGCAAGATTCTTAGGAAGGACCTGAGAGCGCGGCTTG

Basic information

species Zea mays
transcript GRMZM2G055320_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055320_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g44620.1 (Oryza sativa), 3'ss of exon 5
gtaataccaaatcttgactttcataatcaacacagttgttatatatcggtgcatgtctacaaacatgtaaaaacataagaagtattttgcctatgcactagaaaggcaaaacactaggatccaaacttcccgaagactccataccttatcacggtttctaccatgttatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCGAAGAATCCCTCCGGCAAGATTCTTAGGAAGGACCTGAGAGCGCGGCTTG
                                                         ||||  |||| | || |||| ||| || || |  |            | | | | || |   |   | | |    |  |    |  ||  ||    ||||  | ||    |  | | |||| || |||||||||||| |||||| |||||||||| ||||||| || ||||||| ||| || ||||||||||| ||||||||||| |||||   |||||
--------------------------------------------------------atacat-catgcagaagcata-gaaataattggattg-----------gtccatataccaatgtttcaccgttataagcatcataatccagatt---gttttgaaca----acatcacagGTTGTTTTCTACAAGAGGCTCAACAAAGTTTTCTTCGCGGATTCAATTCCGAAGAGTCCTTCTGGCAAGATTCTCAGGAAGGACCTCAGAGCAAAGCTTG
















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|211370703|gb|FL471723.1|FL471723
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|211365922|gb|FL274320.1|FL274320
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|120481105|gb|EH211167.1|EH211167
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|14242682|gb|BG840387.2|BG840387
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|14202260|gb|BG835937.1|BG835937
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|4826223|gb|AI667851.1|AI667851
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|211119687|gb|FL454266.1|FL454266
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|211033456|gb|FL445334.1|FL445334
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|76911495|gb|DV164298.1|DV164298
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|28984816|gb|BQ539233.2|BQ539233
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|18165720|gb|BM335559.1|BM335559
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|18174018|gb|BM349406.1|BM349406
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|45568106|gb|CK985905.1|CK985905
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|211119688|gb|FL454267.1|FL454267
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|67019027|gb|CO447776.1|CO447776
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|7958402|gb|AW862704.1|AW862704
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|149000216|gb|EE037361.2|EE037361
EST:     AAGGCTTTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTTTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
EST: gi|76924614|gb|DV170050.1|DV170050
EST:     AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAG                         GTCGTGTTTTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG
genomic: AAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCG

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: 44 (upstream exon), 42 (downstream exon)
Score: 40

GAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAGTGAAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCGAAGAATCCCTCCGGCAAGATTCTTAGGAAGGACCTGAGAGCGCGGCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 76

GAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAGTGAAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCGAAGAATCCCTCCGGCAAGATTCTTAGGAAGGACCTGAGAGCGCGGCTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 95

GAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAGTGAAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCGAAGAATCCCTCCGGCAAGATTCTTAGGAAGGACCTGAGAGCGCGGCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 346

GAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAGTGAAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAGGAGgtaataccaa ... tatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCGAAGAATCCCTCCGGCAAGATTCTTAGGAAGGACCTGAGAGCGCGGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaacttcccgaagactccataccttatcacggtttctaccatgttatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCGAAGAATCCCTCCGGCAAGATTCTTAGGAAGGACCTGAGAGCGCGGCTTG
                                            ttatgttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataccaaatcttgactttcataatcaacacagttgttatatatcggtgcatgtctacaaacatgtaaaaacataagaagtattttgcctatgcactagaaaggcaaaacactaggatccaaacttcccgaagactccataccttatcacggtttctaccatgttatgttatagGTCGTGTTCTACAAGAGGATCAACAGAGTTTTCTTCACGGATTCTATCCCGAAGAATCCCTCCGGCAAGATTCTTAGGAAGGACCTGAGAGCGCGGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA