Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgatctgtttgtgcttgattattaagcccttatatccttgaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

Basic information

species Glycine max
transcript GLYMA10G04480.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 8
catgatctgtttgtgcttgattattaag--cccttatatccttgaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA
   |    | |||  ||||  | |  ||     ||| | | ||     ||||     |  |   |     ||    ||  | |  || | ||   |  ||||||| ||||||| || || || || || || |||||| | |||||||||||||||||||||||||| || ||||| || |||||||| |||||||| || |
-gaggatggcttg-acttgcctctggagggatgttacagcttttgttgttctgagaatggaaactgaagatatttatgagtttatctctaatacctttacagGTGGCTGCTGCCAAAGCTGACTTGAACTACATTGGGCTTGATGGAGAAATTGGCTGCATGGTGAACGGTGCAGGATTGGCAATGGCTACAATGGACATCA

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------------catgatctgtttgtgc-----ttgatta---ttaagcccttatatcctt---gaaccttcttt----------ctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA
                                                         | || ||||| |||     |||| |    || || |||||| | |     |||| | | |           ||||||  || || | |||  |              ||   || ||||||  ||||||| || |||||||| || ||||||||  | |||||||| ||||| |||||||||||||||||||| || || ||||| || |||||||| |
gtataaaattacctatctttccatttgttcattctctccttgtgtcaagttttcttctaatgtgtttttgcacattttgacttccttttagtccttatttgcgatgagaacttgcctcttagctagtacttttttttggttatataatctcagcaccagaaccaatacctgtacagGTCGCTGCTGCCAAAGCAGATTTGAACTATATTGGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTA

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G064695_T03 (Zea mays), 3'ss of exon 7
catgatctgtttgtgcttgattattaagcccttatatccttgaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA----------------------------------
                              |||   || | |     |  | ||||||  || || | |||  |              ||   || ||||||  ||||||| || |||||||| || ||||||||  | |||||||| ||||| |||||||||||||||||||| || || ||||| || |||||||| |                                  
------------------------------cttgcctcttag----ctagtacttttttttggttatataatctcagcaccagaaccaatacctgtacaggtcgctgctgccaaagcagatttgaactatattgGTCTTGATGGAGAGATTGGTTGCATGGTGAATGGAGCAGGATTGGCCATGGCGACCATGGATATTATAAAGTTGCATGGTGGTACGCCCGCCAATTTTCT

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------------------------------------catgatctgtttgtgct-tgattattaagcccttatatccttgaaccttctttctttttactgtt---tgtgtaacattgtatgtgccttttatctttg-aacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA
                                                          |  |  |||   | |  | |     |  ||| | | | |   |        |     ||  |     | |||||  || ||| ||   |||  || |  || ||||| ||||||| || |||||||| || || || || ||||||||||||||||| |||||||||||||| || || ||||||||||| || ||||||||||
gttgggttacttcttttaatttcttgaccctgttttatctgtgatgtaagtggaaagtagcacatgtacataccataaaggcaatccccctctcttcacaactacaaggtaaaactaaagaacaatatgtaatgttctatttgtggtttcactgtacaatagGTGGCTGCTGCCAAAGCAGATTTGAACTACATCGGCTTAGATGGAGAAATTGGTTGCATGGTGAATGGTGCTGGCTTAGCAATGGCTACCATGGATATAA

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S9_103V6.2 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------catgatctgtt----tgtgcttgattattaagcccttatatcctt---gaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA
                                      |  |||||||    ||  |||  | ||       |||| | |||    |||  |||   ||  | |   ||   |    |||   ||| | |   |   |    ||||  |||||| |||||  ||  | ||||| || || || ||||| |||||||| ||||||||||||||||| ||| | |||||||| ||||||||||| |
gtttgttgtagacagcttagtacttttctgtatgatataacatctgttgaactgcactttgtaatacgaagattatctgctttggaaacaatctcaattacttccagtttgatggacttgccagtgtcgtggtttcct---tagGTTGCTGCTGGAAAGGTGGACCTGAATTACATAGGATTGGATGGTGAAATTGGATGCATGGTGAATGGAGCGGGGCTTGCAATGGCTACAATGGATATCA

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ13492 (Selaginella moellendorffii), 3'ss of exon 8
catgatctgtttgtgcttgattattaagcccttatatccttgaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA
                                               | |      ||  |  | || | || || ||  ||||| ||  |    |||||||  |||||||    || ||||| || || ||||| || ||||| || ||||||||||||||||||||||||||  | || ||||| || |||||||| |
----------------------------------------------gtttgagaccttgttcatagtttcacgtttta-atgcctgtt--cgaaaaacagGTCGCTGCTGCTGCCGCCGATTTGAACTACATTGGATTGGATGGCGAGATTGGCTGCATGGTGAATGGAGCAGGACTCGCGATGGCAACCATGGATATCA

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|208273318|gb|GE070590.1|GE070590
EST:     AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAG                         GTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
genomic: AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAGgtttacttct ... ctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
EST: gi|17518793|gb|BM187835.1|BM187835
EST:     AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAG                         GTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
genomic: AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAGgtttacttct ... ctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
EST: gi|254325002|gb|GR834427.1|GR834427
EST:     AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAG                         GTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
genomic: AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAGgtttacttct ... ctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
EST: gi|15000418|gb|BI321232.1|BI321232
EST:     AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAG                         GTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTA
genomic: AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAGgtttacttct ... ctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTA
EST: gi|298179372|gb|HO027843.1|HO027843
EST:     AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAG                         GTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
genomic: AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAGgtttacttct ... ctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
EST: gi|151406201|gb|EV276016.1|EV276016
EST:     AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAG                         GTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
genomic: AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAGgtttacttct ... ctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
EST: gi|6727069|gb|AW311423.1|AW311423
EST:     AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAG                         GTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT
genomic: AGAAAGAGATATTTTCTCTCCGTGATACAACACAAGAGGACCCTCGAGAGgtttacttct ... ctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA
                    gtgtaac  putative branch site (score: 3)
                                   tgccttttatcttt  putative PPT
                                       ttttatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgatctgtttgtgcttgattattaagcccttatatccttgaaccttctttctttttactgtttgtgtaacattgtatgtgccttttatctttgaacagGTGACTGCTGCAAAGGCAGATTTAAATTATATTGGGTTAGATGGAGAAATTGGCTGCATGGTGAATGGAGCAGGGTTAGCAATGGCCACAATGGATATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
catgatc
- - - - - - -tgcttga
- - - - - - - - - - - - - agccctt
- - - - - - - - - - - - - - - - - - -ccttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtgc