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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA

Basic information

species Glycine max
transcript GLYMA19G30100.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattg-gtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
                                ||  || | ||  ||  | |      ||   | ||| ||  ||||  | |  ||| | |  | | |  |||  |  |    |     ||||| ||||| ||||||| || || |||||||||||||| ||||||||| | |||||||| |||||||| || ||||||||||| || ||||| || || || ||||
--------------------------------gtgcttatacaagtttctctagtcaattggttttctttacatattctgcagtcatta-ctctaattattttgctcgtaacttct--tcctgt-agATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
                                              |  || ||   ||||| |    || | |  ||  ||  ||  || |||  | ||| | | |  || ||     ||| ||||||||||||||||| || |||||||| ||||||||||||||| | |||||||| |||||||| || ||||||||||| || ||||| || ||||| ||||
---------------------------------------------gtccttggatcatttctttcatagtctttgatgcaataaatttgc-ttgtattattaaattacattctta----ctggcagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAAATACAAA

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
                                              |  || ||    || | ||  | ||    | | |  |  | ||  |||  |   ||||| | || | |     ||| |||||||||||||| || || |||||||| ||||||||||||||| | |||||||| |||||||| || || |||||||| || ||||| || ||||| ||||
---------------------------------------------gttcttggatcacttatttagttatagtcttcgatg-cagtaagt-ttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgt-cagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
|||   | ||||   | | ||    |    | |  |  |||| |||   ||   ||||  |  ||| | ||| ||      |  ||     |   || || ||  ||||||  || || |||  ||||| ||||| ||||||||||||||||||| ||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||||| || |||||||
gtatttttttagccctgtttg----gtcagatgacgcattcctgctctgttctcatgtgcccttatatatatgtaaaacattttat-----tatggtaatctaaggatttt--tggacactgaacagATTTTGAAAGAACTTCACAAATCTTGTCGAAGAGAAGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAA

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
             | |   ||  ||     ||  |||| |  ||  ||| ||  ||  ||      ||| |||  |  ||| |        |   |      | || |  |||         | |||| |||||||| ||||||||||||||||||| ||||||||| |||||||| || ||||| || || || ||  |||| |||||||| || |||||||| |
-------------actccttggtatacatcag--tgttatgtagaataacttttatagttgca---ctgcatc-gtcagtagcatcatatgtgatgctgaccaatggtcgtgt-------gtttagATCTTGAAGGAGCTTCACAAATCTTGTCAAAAGGAAGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGA

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------gtaacatattagtattttgtgcaatggtgtagg---ttgttttccagcttaatttgaatgtttctgtatc---tgta-tctattggtatccatgagcattgagtgatttattgat-tttgttgaaccctgt-----cagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
                                    | | || ||   | ||| |  | |  || | |   | |||| |  |    |   | |  ||||   ||    |||| | | | |  |       |   ||||  |  |  ||||  |    |      ||     ||||| |||||||| || || ||||||||||| | |||||||||||||||||| || ||||| || || ||| |  ||||||| ||||| ||||| ||||| |
gtaagtattctgcccgttgactcctcaactttattttcatatctttcaactttatctagtattgaatgatttcgtttactcggaataccagtacttttcaaaatgggatgtaatgtgtagtaaattccttgttctgagaaaacttgtgatactcacagcttgtcgtacgtgcagATTTTGAAGGAGCTCCATAAATCTTGTCAGAAGGAAGATGGTACAGATGACCAGAAGAAGGGCACACAATTGCTGGAGGTGTATGCGATAGAGATTCAGA

upper sequence: GLYMA19G30100.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------gtaacatat-tagtattttgtg-caatggtgtaggt---tgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
                                              ||   ||| |  || |   || || | |  ||  |   || ||| ||| |  |  |  |||||     |  | ||| | || |||  ||  |   |    || ||   | ||||  | ||||     ||||| |||||||| || |||||||||||||| |  |||||||||||||||||||| ||||| || || ||| |  | ||||||||||| ||||| ||||| |
gtaagttcgctgccagttgatttctccacaatatcttcatatgtcctattttatctgataataaatgtcagtcgcttatctcaatgcttttcagttcgagatatatgttcgcagaa-tatattttttcgta--cacaaatgtgagatgctt--ctaatttcttagaactg---cagATTTTGAAGGAGCTCCACAAATCTTGTCAGAAAGAAGATGGTACAGATGATCAGAAGAAGGGCACACAATTGCTCGAGGTTTATGCGATAGAGATTCAGA

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|192319385|gb|FK009927.1|FK009927
EST:     AGCTTTGTAAGATCTTCTTTGATATTGGGGAATATGGGCGGATGAGTAAG                         ATATTGAAGGAACTTCACAAATCTTGTC
genomic: AGCTTTGTAAGATCTTCTTTGATATTGGGGAATATGGGCGGATGAGTAAGgtaacatatt ... accctgtcagATATTGAAGGAACTTCACAAATCTTGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA
                              tattgat  putative branch site (score: 3)
                                              ccctgtc  putative PPT
                           atttattgattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatattagtattttgtgcaatggtgtaggttgttttccagcttaatttgaatgtttctgtatctgtatctattggtatccatgagcattgagtgatttattgattttgttgaaccctgtcagATATTGAAGGAACTTCACAAATCTTGTCAAAGGGAAGATGGTACAGATGATCACAAGAAAGGAACCCAACTTTTGGAGGTTTATGCAATAGAAATTCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG