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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtttttgttgttggaaatctaaggctatttgatattacaaactccttgctacttcaaatggtttggtgagaactaacagtttccatacaaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGTTGTCTGTTGATGATTTACTGTTTCAAACAAGAATAGTAGCATCACTTAT

Basic information

species Zea mays
transcript GRMZM2G382240_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G382240_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 9
--------------tatgtttttgttgttggaaat--ctaaggctatttgatattacaaactccttgc---tacttca-aatggtttggtgagaactaacagtttccatacaaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGTTGTCTGTTGATGATTTACTGTTTCAAACAAGAATAGTAGCATCACTTAT--
                || |   | ||||    |   | | |  |||   ||   ||      ||||     |   || ||    ||  ||| || | ||  ||||  ||||||   ||||||||||| |||  ||||||||||||||||| ||||||||||||||||| |||||||||||   || |  ||||        ||  ||  ||    | |   
gtatgtcatacagacttgatcaagctgttttttactgccacgtatatgcaatgcaacttctgtcttgtgaacatgccataacaagttactgacaagttac--tttctgtacaaaatgcagAGTTCTAACCCCGGCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAATTGTCTGTTGACATTTGATAGTTTACTGTTCTAA--GTGACACTCTTGAGCC
















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|108954176|gb|EC365039.1|EC365039
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT
EST: gi|6851609|gb|AW352619.1|AW352619
EST:     TCCTCCANCAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT
EST: gi|29945873|gb|CB815863.1|CB815863
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGCCCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAA
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAA
EST: gi|9953260|gb|BE639843.1|BE639843
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT
EST: gi|211467417|gb|FK984374.1|FK984374
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT
EST: gi|29543478|gb|CB605564.1|CB605564
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT
EST: gi|32944790|gb|CF049609.1|CF049609
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT
EST: gi|6993991|gb|AW453205.1|AW453205
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT
EST: gi|5555273|gb|AI881224.1|AI881224
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT
EST: gi|15352985|gb|BI502596.1|BI502596
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT
EST: gi|6828067|gb|AW331710.1|AW331710
EST:     TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAA                         AGTTCTAAGCCCATCAGAGATCAAGGATTTCTTGGAAGAGGTGGAGTAAGT
genomic: TCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGT

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 12 (downstream exon)
Score: 4

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGTTGTCTGTTGATGATTTACTGTTTCAAACAAGAATAGTAGCATCACTTAT


Block sizes: 45 (upstream exon), 11 (downstream exon)
Score: 3

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGTTGTCTGTTGATGATTTACTGTTTCAAACAAGAATAGTAGCATCACTTAT


Block sizes: 40 (upstream exon), 10 (downstream exon)
Score: 1

ATATGAGGGGCAAATTTCCTCCAACAACATTGAAATCGGAATTATTCGAGCTGACCGTGAGTTCAAgtaagttaca ... caaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGTTGTCTGTTGATGATTTACTGTTTCAAACAAGAATAGTAGCATCACTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttgctacttcaaatggtttggtgagaactaacagtttccatacaaataacagAGTTCTAAGCCCATCAGAGATCAAGGATTTCATGGAAGAGGTGGAGTAAGTTGTCTGTTGATGATTTACTGTTTCAAACAAGAATAGTAGCATCACTTAT
                            aactaac  putative branch site (score: 1)
                                          atacaaataa  TA-rich tract