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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttttcccagccaaaagtctctgtcaaaatgaatatgttaagtcttatttgtagtaccatcttcatttcctctgatggttattgttcttttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCACTAATTCAACTGCCACAGAATCGTCACCTGTTGCTGGCCCTCAAGAGGA

Basic information

species Zea mays
transcript GRMZM2G150212_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150212_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g31470.1 (Oryza sativa), 3'ss of exon 5
----gtttttttcccagccaaaagtctctgtcaaaatgaatatgttaagtcttatttgtagtaccatct---tcatttcctctgatgg---ttattgttcttttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCACTAATTCAACTGCCACAGAATCGTCACCTGTTGCTGGCCCTCAAGAGGA---
    ||  |||    |  |  || |||||  || ||     || || |||| | |  || ||| ||  |   | |    |||  ||||   |  ||| ||||| ||||| ||  ||| | || |||||| | |||| ||||||||| ||||| || |||||   ||||||||||||    |||||||||||||||||||| ||||||||  |   
gtttgtgctttcttaaaactgaaatctctaccacaacatg-atatttagtcctttcggttgtaacaaataactgagaaactccaatggaactctttgatctttggtacagAG--GCCCTAGAGGAACAACGAATTATTCTAGCTGCTGCTGCAGCAGCAGC---TAATTCAACTGCTGGGGAATCGTCACCTGTTGCTGGTCCTCAAGAAAATGA
















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|60348163|gb|DN215136.1|DN215136
EST:     TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAG                         CTGCCTTGGAAGAACAAAGGATTACTCTAGCTGTCGCTGCGGCTGCAGCCA
genomic: TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAGgtttttttcc ... ttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
EST: gi|91048015|gb|EB158433.1|EB158433
EST:     TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAG                         CTGCCTTGAAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
genomic: TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAGgtttttttcc ... ttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
EST: gi|211341570|gb|FL066576.1|FL066576
EST:     TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAG                         CTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
genomic: TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAGgtttttttcc ... ttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
EST: gi|60341697|gb|DN208670.1|DN208670
EST:     TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAG                         CTGCCTTGGAAGAACAAAGGATTACTCTAGCTGTCGCTGCGGCTGCAGCCA
genomic: TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAGgtttttttcc ... ttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
EST: gi|32795270|gb|CD947506.1|CD947506
EST:     GATCTGATCACAACAAGTGAAGGGCTACAAG                         CTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
genomic: GATCTGATCACAACAAGTGAAGGGCTACAAGgtttttttcc ... ttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
EST: gi|211341571|gb|FL066577.1|FL066577
EST:     TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAG                         CTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
genomic: TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAGgtttttttcc ... ttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
EST: gi|211341572|gb|FL066578.1|FL066578
EST:     TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAG                         CTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA
genomic: TCTTGATCTCTTGGAGCTAGATCTGATCACAACAAGTGAAGGGCTACAAGgtttttttcc ... ttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttgtagtaccatcttcatttcctctgatggttattgttcttttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCACTAATTCAACTGCCACAGAATCGTCACCTGTTGCTGGCCCTCAAGAGGA
                         ctctgat  putative branch site (score: 4)
                                     ttgttctttt  putative PPT
                                  ttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttttcccagccaaaagtctctgtcaaaatgaatatgttaagtcttatttgtagtaccatcttcatttcctctgatggttattgttcttttgtacacagCTGCCTTGGAAGAACAAAGGATTACTCTAGCTGCCGCTGCGGCTGCAGCCACTAATTCAACTGCCACAGAATCGTCACCTGTTGCTGGCCCTCAAGAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA