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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattgcaaatataaaaaccatcattatttttttattaattctttttaatcctcaactgttttctgctaatagttgagaacagattgtggttctcctttatttatttattttctccttgaaactgccactgtctaaatactatattttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT

Basic information

species Zea mays
transcript GRMZM5G871336_T01
intron # 4
splice site 3'
intron type U2

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|71430125|gb|DR811175.1|DR811175
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|211068146|gb|FL037286.1|FL037286
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|211070875|gb|FL037292.1|FL037292
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|71432140|gb|DR813190.1|DR813190
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|71311972|gb|DR792494.1|DR792494
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|148950551|gb|EC896128.2|EC896128
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|13381878|gb|BG458553.1|BG458553
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|93012464|gb|EB637984.1|EB637984
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|149059964|gb|EE157094.2|EE157094
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|149045945|gb|EE047943.2|EE047943
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
EST: gi|211070884|gb|FL037301.1|FL037301
EST:     TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTG                         GATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
genomic: TCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT

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: 46 (upstream exon), 48 (downstream exon)
Score: 53

TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 51

TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 32

TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 35

TTGTTTGAAGCCCCTCTTGATGAAAAAGAAATATCGCTACGATATAGCTCTGCTCTTGTTCAAGGTGCTACAAATGTATTTTGgtatgattgc ... ttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttattttctccttgaaactgccactgtctaaatactatattttttttgtagGATTGACATACAGACAAATACAAGACATTTTCTCTCTTTGTATCAT
                             gtctaaa  putative branch site (score: 35)
                                         tatttttttt  putative PPT
                              tctaaatactatattt  TA-rich tract