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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcattcagtacatgtacttattatcggaaaagagaaaagaattatttacaaggcaatagttcaaagttacaaaacttatcttctgtacttcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT

Basic information

species Glycine max
transcript GLYMA19G37750.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 18
---agcatt-cagtacatgtacttattatcggaaaagagaaaagaattatttacaaggcaatagttcaaagttacaaaacttatcttctgtacttcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT
   |  ||| |      ||||    || ||   ||        |  || |||    | ||||| |||    |||    | || | || | |  | | |  |||||| ||||| |||||||| || ||||| || |||||||| ||||||||||| ||||| || || ||  |||| | ||  
aaaaatattactacctttgtaaaagttttctttaatatatgtcgctttgtttg---gtcaataattcgtcattatcggaattgtgttattt-ttacattgtcagGGTGATGCAGACTATCTTAGGTATCATGGTATGCAAGAGTTTGATCAGGCAATGCAACATCTTGAGCAAAAATATGAA

upper sequence: GLYMA19G37750.2 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G073054_T02 (Zea mays), 3'ss of exon 18
-------------------------------------------------agcattcagtacatgtacttattatcggaaaagagaaaagaattatttacaaggcaatagt-----------tcaaagttacaaaacttatcttctgtacttcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT
                                                    |||   |      ||||  | | |||||    || |   || | || |||  |||| |           ||   |||    ||   |  ||   | | | ||  |||||| ||||| || ||||| |||||||  || |||||||| ||||| ||||| ||||||||||| || | ||| | ||  
gtaagtttaactgtgctactatattctttcgacttatctggattgaccacatatttcttggtaaaacttgct-ttggaaagatcaagaatgttctatataagctaatactaccatatgttatcggtgttgttgaatacaattttaatccctttt--tcagGGAGATGCAGATTATCTTAGATATCGTGGTATGCAAGAGTTTGACCAGGCAATGCAGCACCTTGAGGGAAAATATGAA
















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|13789383|gb|BG651974.1|BG651974
EST:     TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTG                         GGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
genomic: TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTGgtaagtccat ... tcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
EST: gi|209702274|gb|BW677969.1|BW677969
EST:     TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTG                         GGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
genomic: TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTGgtaagtccat ... tcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
EST: gi|7283403|gb|AW596011.1|AW596011
EST:     TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTG                         GGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATCTGATCAGGCT
genomic: TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTGgtaagtccat ... tcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
EST: gi|20498242|gb|BQ273172.1|BQ273172
EST:     TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTG                         GGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
genomic: TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTGgtaagtccat ... tcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
EST: gi|15285214|gb|BI469105.1|BI469105
EST:     TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTG                         GGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
genomic: TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTGgtaagtccat ... tcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
EST: gi|207706010|gb|GD687842.1|GD687842
EST:     TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTG                         GGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT
genomic: TTCCAGGGAATAACAACAGTTTTGACAAGTGCAGGCGTAGATTTGACTTGgtaagtccat ... tcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacaaggcaatagttcaaagttacaaaacttatcttctgtacttcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT
                                  tcttctgtacttctt  CT-rich tract
                          aaaacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcattcagtacatgtacttattatcggaaaagagaaaagaattatttacaaggcaatagttcaaagttacaaaacttatcttctgtacttcttaatcagGGCGATGCGGACTATCTAAGATATCAAGGGATGCAAGAATTTGATCAGGCTATGCAGCACCTAGAAGAAAAGTTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA