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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttcagaccacgcggccttcgttctcccgttatttggattttgttctgatcagttgggtctgttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGTCTCAGTG

Basic information

species Zea mays
transcript GRMZM2G162284_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162284_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g37910.3 (Oryza sativa), 3'ss of exon 2
gtgagtttcagaccacgcggccttcgt--------tctcccgtt--atttggattt---tgttctgatcagtt---gggt-ctgttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGTCTCAGTG
|||||| | ||| |    ||  || ||        |   |||||  |  ||| |||    |||||||||  ||   ||||  |||||||||||||||| |||||||||||||||||||||||||||||||||| || || || ||||| |||
gtgagtcttagatccgtgggtttttgtgttagtggttctccgttcgaagtggttttgggcgttctgatcgatttgggggtgttgttttttgcagGGAGCAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAACGTCAAGCAGGTCTCGGTG
















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|22472639|gb|BU037119.1|BU037119
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|31359518|gb|CD443875.1|CD443875
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAGGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|67015235|gb|CO443984.1|CO443984
EST:     GCCTCCGACCGCGTTCTCTC-TCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAGCAAGT
genomic: GCCTCCGACCGCGTTCT-TCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|211010350|gb|FL233636.1|FL233636
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|14203924|gb|BG837601.1|BG837601
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|26558436|gb|CA830671.1|CA830671
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|21891488|gb|BQ744701.1|BQ744701
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|211010348|gb|FL233634.1|FL233634
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|211010355|gb|FL233641.1|FL233641
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAGCAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|71436984|gb|DR818034.1|DR818034
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|211010351|gb|FL233637.1|FL233637
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|211010356|gb|FL233642.1|FL233642
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCACGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAGCAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|4874486|gb|AI674006.1|AI674006
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGNCCGCGTTTTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCNCCCCAATGTGAANCAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|78112438|gb|DV530832.1|DV530832
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|33100122|gb|CF060082.1|CF060082
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCACGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAGCAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|87155374|gb|DY400163.1|DY400163
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT
EST: gi|211010354|gb|FL233640.1|FL233640
EST:     AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCACGTTCTTCGTCTTCAT                         GGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAGCAAGT
genomic: AAGGACCCAAACAAGCCCAAGAGGCCTCCGACCGCGTTCTTCGTCTTCATgtgagtttca ... ttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgttctcccgttatttggattttgttctgatcagttgggtctgttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGTCTCAGTG
                          ttctgat  putative branch site (score: 3)
                                         tctgtttttt  putative PPT
                    attttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttcagaccacgcggccttcgttctcccgttatttggattttgttctgatcagttgggtctgttttttgcagGGAGGAGTTCAGGAAGGACTACAAGGAGAAGCACCCCAATGTGAAACAAGTCTCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC