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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGGTTCATCCTCTGAAGGTTTCTCTGGAGGATTTGTACAATGGCACATCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatctgaatccacaacacaaggatgccaaaaactcaattacaatatgctttctatattagattcttaggatctgattgtgtgcttgtaatcgtgcag

Basic information

species Zea mays
transcript GRMZM2G028218_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028218_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G31620.2 (Glycine max), 5'ss of exon 3
ATGTGGTTCATCCTCTGAAGGTTTCTCTGGAGGATTTGTACAATGGCACATCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatctgaatccacaacacaaggatgccaaaaactcaattacaatatgctttctatattagattcttaggatctgattgtgtgct---tgtaatcg---tgcag
||||||||||||| |||||||| |||||||||||| | |||   || ||||| ||||| |||||||| || || || || || || || || ||||||||||  ||  | || |     |  |     ||   ||  ||    ||    |    |||   || |||  | || |    || | || || |   ||||||     | |||
ATGTGGTTCATCCCCTGAAGGTCTCTCTGGAGGATCTTTACCTCGGAACATCTAAGAAACTCTCTCTTTCACGAAACGTGCTGTGTTCAAAATGCAATGGgtgtgtgttgtgca-----attaggtttatataaaggacatgcttgttgttcctttttgttaatagggtttttgacattgttggtttgttgtatgtaatttgattacag

upper sequence: GRMZM2G028218_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G38790.1 (Glycine max), 5'ss of exon 3
ATGTGGTTCATCCTCTGAAGGTTTCTCTGGAGGATTTGTACAATGGCACATCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatctgaatccacaacacaaggatgccaaaaactcaattac-aatatgctttctatattagattcttaggatc--tgattgtgtgcttgtaatcgtgcag------
||||||||||||| |||||||| |||||||||||| | |||   || || |||||||| |||||||| || || || ||  | ||||| || ||||||||||  ||  |  | |   |           |   ||   |  | ||    ||    ||| |  ||  | || ||   ||   |||||   ||  |||||| |   |       
ATGTGGTTCATCCCCTGAAGGTCTCTCTGGAGGATCTTTACCTCGGAACTTCAAAGAAACTCTCTCTTTCACGAAACGTGTTGTGCTCAAAATGCAATGGgtgtgtgttgcgcaattaggttttg----tttgaagggcatacttgttgatcctttttgttaatagggtttttgacattgttgatttgttgtatgtaattgattacttacag

upper sequence: GRMZM2G028218_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0073g00560.t01 (Vitis vinifera), 5'ss of exon 4
ATGTGGTTCATCCTCTGAAGGTTTCTCTGGAGGATTTGTACAATGGCACATCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatctgaatccacaacacaaggatgccaaaaactcaattacaatatgct----ttctatattagattcttaggatctgattgtgtgcttgtaatcgtgcag
| ||  | || || || |||||||||||||| ||| | |||||||| ||||| ||||| || || || || || |||||  ||||||| |||||||| ||||  ||       || ||  |  |   | |  |   |  |   |  |   ||  |     | | | |  || |  ||   | | ||  |  |  ||  |   |||||
ACGTCATCCACCCCCTTAAGGTTTCTCTGGAAGATCTCTACAATGGGACATCCAAGAAACTGTCCCTTTCTCGTAATGTAATCTGCTCAAAGTGCAAGGGgtgagtacaaactatgcagtattctcagttttctgcagtttcgtgtctgcatcttatgactttgtttgtgacttatattgtatcatgattggggtgataatttgcag

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|40336876|gb|CK370946.1|CK370946
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|67030348|gb|CO459097.1|CO459097
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|31360427|gb|CD444784.1|CD444784
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|5566927|gb|AI881838.1|AI881838
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|211088782|gb|FK991008.1|FK991008
EST:     CAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTNCCA-GTGCAATGG                         TAAGGGTTCCAAGTTTGGAGCT
genomic: CAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCT-CCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCT
EST: gi|22521136|gb|BU079947.1|BU079947
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTT
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTT
EST: gi|9743001|gb|BE519149.1|BE519149
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|211531690|gb|FK990937.1|FK990937
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTTTGGAGCTTTCGTCGAGGTTGTG-TGGGGTTGGTCAA
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTT-CGTCGAGGT-GTGCTGG--TTG-TCAA
EST: gi|67035410|gb|CO463943.1|CO463943
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|211531686|gb|FK990933.1|FK990933
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCNAGTGCAATGG                         TAAGGGTTCCAAGTTTTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTT
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCT-GGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTT
EST: gi|51592714|gb|CV071860.1|CV071860
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|5268675|gb|AI770639.1|AI770639
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|32845319|gb|CD985000.1|CD985000
EST:     TCAAAAAAGCTCTCTCTGTCCCGCAATGTCCTTTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|87155560|gb|DY400349.1|DY400349
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|28361755|gb|CB240111.1|CB240111
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|26559272|gb|CA831507.1|CA831507
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|211091233|gb|FK991021.1|FK991021
EST:     CAAAGAAGCTCTCTCTGTCCCCGCA-TGTCCTCTGCTCCA-GTGCAATGG                         TAAGGGTTCCAAGTTTGGAGCTTCCTCGAGGGG-GCTGGGTGTCAAGGTTC
genomic: CAAAGAAGCTCTCTCTGTCCC-GCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|67038376|gb|CO464706.1|CO464706
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|7162265|gb|AW519872.1|AW519872
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|211534686|gb|FK990945.1|FK990945
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTTTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|5268935|gb|AI770899.1|AI770899
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|28361546|gb|CB239902.1|CB239902
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|5555500|gb|AI881451.1|AI881451
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|32836749|gb|CD976427.1|CD976427
EST:     TCAAAAAAGCTCTCTCTGTCCCGCAATGTCCTTTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
EST: gi|8368444|gb|BE051389.1|BE051389
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAG
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAG
EST: gi|211540708|gb|FK990973.1|FK990973
EST:     TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGG                         TAAGGGTTCCAAGTTTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC
genomic: TCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatc ... aatcgtgcagTAAGGGTTCCAAGTCTGGAGCTTCGTCGAGGTGTGCTGGTTGTCAAGGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGGTTCATCCTCTGAAGGTTTCTCTGGAGGATTTGTACAATGGCACATCAAAGAAGCTCTCTCTGTCCCGCAATGTCCTCTGCTCCAAGTGCAATGGgtaggtcatctgaatccacaacacaaggatgccaaaaactcaattacaatatgctttctatattagattcttaggatctgattgtgtgcttgtaatcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC