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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgtgagcttccaaagaaacactatattcttgaaacttcattgtgattgccaatgtaaccttgtgcggttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTTACATCCACACTTCTCGAGAATGG

Basic information

species Zea mays
transcript GRMZM2G025231_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 7
gtaactgtgagcttccaaag-aaacactata--------ttcttgaaac---ttcattgtgattgccaatgtaaccttgtgcggttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTTACATCCACACTTCTCGAGAATGG
|||   |||| ||||  ||  ||||| | |         ||| ||||||   ||  | || || ||  || ||| | |      ||    | ||||||||| ||||||||||| ||||||||||||||||| ||  | ||||||||||||||||||||||||||||||||  ||||||||||||| ||||||||
gta--cgtgaacttctgaactaaacattgtgggtggtttttcctgaaacacctttgtagtaatagcatatttaatccttcaatatttttggcagGAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTCGCATCCACACTTCTTGAGAATGG
















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|211310943|gb|FL374710.1|FL374710
EST:     GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAG                         GAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
genomic: GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
EST: gi|211147734|gb|FL419640.1|FL419640
EST:     GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAG                         GAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
genomic: GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
EST: gi|211219468|gb|FL394125.1|FL394125
EST:     ACCAATCCCCTGCATATGCTCTTGGTSAAATTGACGAAGCTGCTCCAG                         GAGCTGAGAATNAAAAGGCCGGTATTGTAAATCAACAAAAATTASRAAAGA
genomic: ACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
EST: gi|32850633|gb|CD990314.1|CD990314
EST:     GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAG                         GAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
genomic: GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
EST: gi|32941882|gb|CF046701.1|CF046701
EST:     ACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAG                         GAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
genomic: ACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
EST: gi|211275142|gb|FL390045.1|FL390045
EST:     GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAG                         GAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
genomic: GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
EST: gi|211159525|gb|FL378589.1|FL378589
EST:     GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAG                         GAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA
genomic: GAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGA

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: 78

ACCAAACCCAAAACAGAGAAGAAAAAGTTATTATTTTTCAAGAAAGAAGAGAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTTACATCCACACTTCTCGAGAATGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 243

ACCAAACCCAAAACAGAGAAGAAAAAGTTATTATTTTTCAAGAAAGAAGAGAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTTACATCCACACTTCTCGAGAATGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 110

ACCAAACCCAAAACAGAGAAGAAAAAGTTATTATTTTTCAAGAAAGAAGAGAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTTACATCCACACTTCTCGAGAATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 821

ACCAAACCCAAAACAGAGAAGAAAAAGTTATTATTTTTCAAGAAAGAAGAGAACCAATCCCCTGCATATGCTCTTGGTGAAATTGACGAAGCTGCTCCAGgtaactgtga ... ttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTTACATCCACACTTCTCGAGAATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattcttgaaacttcattgtgattgccaatgtaaccttgtgcggttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTTACATCCACACTTCTCGAGAATGG
                             atgtaac  putative branch site (score: 821)
                                             ttccctgt  putative PPT
                            aatgtaa  TA-rich tract