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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttccaaaccctctcctctcttctctacaggtgtcacctagtcccctctctttcttcaccacccaccaattgctcgatcaatttccccacccggatcaactactgcttcatccatggaccctttcttgctcgagcaattacttcagcgaagcaaatattcttgccttaattcatttacttcctcgttctatggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT

Basic information

species Zea mays
transcript GRMZM2G177914_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g12710.1 (Oryza sativa), 3'ss of exon 2
gttccaaaccctctcctctcttctctacaggtgtcacctagtcccctctctttcttcaccacccaccaattgctcgatcaatttccccacccg-gatcaactactgcttcatccatggaccctttcttgctcgagcaattacttcagcgaagcaaatattcttgccttaattcatttacttcctcgttctatggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
                | ||   |||||     ||||| |  ||||||   |  |   ||||||  ||| |||| | |||||||||||||||  || |||   | ||||     || |||    |  |  | || || ||   ||  |    |   |||   | |  |  |||||  | |     | |   |||  |||||| ||||||||||||||||||||||||||| | |||||||| |
---------------gtttcgattctaccccgttcaccca--cccctccaatcttcgcccacccgacaagtgctgggtcaatttccccacccaagaccaatagcagcttacgtgattgacgaaatgct-tttgaccactttgctctccccttc---tatctattctctgcttcatggatt-----ggttattggatgcagCCCCCCGAGAAGCATCAGGACCTCGTCCGCGGCGTCTTCCAGT
















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|211467101|gb|FK972980.1|FK972980
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211469618|gb|FK972985.1|FK972985
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|19822213|gb|BQ048237.1|BQ048237
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211469620|gb|FK972987.1|FK972987
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211467096|gb|FK972975.1|FK972975
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211469627|gb|FK972994.1|FK972994
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211469622|gb|FK972989.1|FK972989
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTC-GCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|149090359|gb|EE179665.2|EE179665
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211467090|gb|FK972969.1|FK972969
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211469619|gb|FK972986.1|FK972986
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211467098|gb|FK972977.1|FK972977
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211467097|gb|FK972976.1|FK972976
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTC-GCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211467089|gb|FK972968.1|FK972968
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTC-GCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|5499044|gb|AI854911.1|AI854911
EST:     TGATCAGCACCCAGGCCATGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCGGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211472147|gb|FK972996.1|FK972996
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211472153|gb|FK973002.1|FK973002
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211472152|gb|FK973001.1|FK973001
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211472150|gb|FK972999.1|FK972999
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211467094|gb|FK972973.1|FK972973
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|26455836|gb|CA827419.1|CA827419
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211467100|gb|FK972979.1|FK972979
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211469628|gb|FK972995.1|FK972995
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211467088|gb|FK972967.1|FK972967
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211469626|gb|FK972993.1|FK972993
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|149073163|gb|EE161440.2|EE161440
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|211469614|gb|FK972981.1|FK972981
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
EST: gi|71429421|gb|DR810471.1|DR810471
EST:     TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAG                         CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
genomic: TGATCAGCACCCAGGCCAAGCCCCGCCTTCTCAAGTTCTACAGTTTCCAGgttccaaacc ... atggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgaagcaaatattcttgccttaattcatttacttcctcgttctatggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT
                   ccttaat  putative branch site (score: 4)
                                 cttcctcgttctat  putative PPT
                     ttaattcatttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccaaaccctctcctctcttctctacaggtgtcacctagtcccctctctttcttcaccacccaccaattgctcgatcaatttccccacccggatcaactactgcttcatccatggaccctttcttgctcgagcaattacttcagcgaagcaaatattcttgccttaattcatttacttcctcgttctatggtcgcagCCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC