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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtactaactcgcctcgtcttcctcccttttcccccaatccacacgaattcgctggcgccgcctggcgcctttgattttgttcgcttttgtcccaacaattttggcgagcgttccgggtgttttaatgtctgttgttgcgactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG

Basic information

species Zea mays
transcript GRMZM2G108225_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108225_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g59040.1 (Oryza sativa), 3'ss of exon 1
gtcagtactaactcgcctcgtcttcctcccttttcccccaatccacacgaattcgctggcgccgcctggcgcctttgattttgttcgcttttgtcccaacaattttggcgagcgttccgggtgttttaatgtctgttgttgcgactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
|||||||      | || | | |||||||   | ||||   |||                  |  |||  |     ||     ||| | | |||    ||  | |   || || |   ||   || | ||| | |||||   || | ||||||||||||||||||| ||||||||||| ||||||||||| ||||
gtcagtatc----caccacctgttcctcctcctccccctcctcc------------------catctgctgttcccga----attctcatgtgtttttacggtctcc-cgtgc-tcgaggagattctgatggccgttgtgctgattccgcagGTGTGCATCTTCTATCTCGTGCTCCGAGCCCTCGACACTGTTG
















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|211235616|gb|FL131352.1|FL131352
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|211062222|gb|FL131347.1|FL131347
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|211235613|gb|FL131349.1|FL131349
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|149098979|gb|EE184992.2|EE184992
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|211062221|gb|FL131346.1|FL131346
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|149089299|gb|EE178514.2|EE178514
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|148959751|gb|EC905647.2|EC905647
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|74240348|gb|DT648262.1|DT648262
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|149000700|gb|EE037914.2|EE037914
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|148941371|gb|EC886282.2|EC886282
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|211062220|gb|FL131345.1|FL131345
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|148954555|gb|EC899993.2|EC899993
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|211062219|gb|FL131344.1|FL131344
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCCGTGCCCTCGACACCGTTS
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCC-GTGCCCTCGACACCGTTG
EST: gi|211235614|gb|FL131350.1|FL131350
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|148966228|gb|EE017184.2|EE017184
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|149010292|gb|EE042121.2|EE042121
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|211235615|gb|FL131351.1|FL131351
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|211235617|gb|FL131353.1|FL131353
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
EST: gi|148940819|gb|EC885646.2|EC885646
EST:     GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCC                         GTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
genomic: GTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG

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), 40 (downstream exon)
Score: 157

GCCCGAGGAGCACTGGGCCTTCGCCTACTCCATGCTCCAGAAGGTGTCCCGTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 84

GCCCGAGGAGCACTGGGCCTTCGCCTACTCCATGCTCCAGAAGGTGTCCCGTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 99

GCCCGAGGAGCACTGGGCCTTCGCCTACTCCATGCTCCAGAAGGTGTCCCGTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 127

GCCCGAGGAGCACTGGGCCTTCGCCTACTCCATGCTCCAGAAGGTGTCCCGTAGCTTCGCTCTCGTCATCCAGCAGCTCGGACCCGAACTCCGCAATGCCgtcagtacta ... gactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaattttggcgagcgttccgggtgttttaatgtctgttgttgcgactgcgcagGTGTGCATCTTCTACCTCGTGCTCCGTGCCCTCGACACCGTTG
                          ttttaat  putative branch site (score: 127)
                        tgttttaat  TA-rich tract