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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagattgatatacctttaagtaacataacagttttacttttacatgtacacactttcaaacataaatgggcacatgcctgattgttaaaacgttccttcttcag

Basic information

species Glycine max
transcript GLYMA07G05230.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05230.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagattgatatacctttaagtaacataacagttttacttttacatgtac---acactttcaaacataaatgggcacatgcctgattgttaaaacgttccttc--ttcag
| ||||||| | || |||| || ||||| || ||||||||||||||||||||||||||||||||| |||| ||  | |  || || ||||||||||| ||||  |    |  | | |  | |     |||  | |  ||  || | | |  |    |   || | ||  |    |  |  |  ||||| ||||    |   |  ||   ||||
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgt--attcctatttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag

upper sequence: GLYMA07G05230.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G330907_T01 (Zea mays), 5'ss of exon 14
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaag--attgatatacctttaagtaacataacagttttacttttacatgtacacactttcaaacataaatgggcacatgc--ctgattgttaaaacgttccttcttcag
| ||||| | | || | ||||| || || || |||||||||||||| |||||||||||||||||| | || || || |  ||||| | ||||||||| ||||  |    |   || |   ||||||   | |     ||||| || || || |   |  |    | || | |||    |||||  ||| || | |  ||             
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTTTACAGCTTTGGAGTTGTCATGCTTGAGCTACTGACAGGACGTAGACCATTTGACAGgtacactccaaccatctgtttttaagcttcct-----ttttagttataaatttggtc-ttgatgatcagatatgccatcatgccactgtttttcatcacag-----------

upper sequence: GLYMA07G05230.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G153393_T02 (Zea mays), 5'ss of exon 2
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagat--tgatatacctttaagtaacataacagttttacttttacatgtacacactttcaaacataaatgggcacatgcctgattgttaaaacgttccttcttcag
| ||||| | | || | ||||| || || || ||||||||||| || |||||||||||||||||| | |||||  | |  ||||| | ||||||||| ||||  |      | || |   ||||||     |   |||| ||  |||   | |  |   |   | |    | ||    |||  | |                        
CAGAAGTGGACATGACCGGTCAGTACACCCTCAAGAGTGATGTCTACAGCTTTGGAGTTGTCATGCTTGAACTATTGACAGGACGTAGACCATTTGACAGgtacactcccatcatctgtttttaagctttcttttagttataaatttg-gtattgatgatcagatatgccactgtttccattacag------------------------

upper sequence: GLYMA07G05230.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G004572_T01 (Zea mays), 5'ss of exon 14
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagattgatatacctttaagtaacataacagttttacttttacatgtacacactttcaaacataaatgggcacatgcctgattgttaaaacgttccttcttcag
| || || |   |||| ||||| ||||| || ||||||||||| || |||||||| || |||||| |||||||  | |  || || ||||||||||| ||||  | |  |   ||  |  ||  |  ||  || |  |||     |  ||  ||  |   |     |   ||  |  |    ||||| | | ||| ||    |     
CTGAGGTCGAGATGTCCGGTCAGTATACCCTCAAGAGTGATGTCTACAGCTTTGGGGTCGTCATGCTGGAACTCTTGACAGGCCGTAAACCATTTGACAGgt--atgcctatcat--cactagatgccagcactgcgttaaacccat-tgcccatgcag-cggtttttggtgacctgac-tatgatt-tcacaacattatcgcag---

upper sequence: GLYMA07G05230.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagattgatatacctttaagtaac--ataacagttttactttt----acatgtacacactttcaaacata--aatgggcacatgcctgattgttaaaacgttccttcttcag--
| || |||| | |||| ||||| |||||||| |||||||||||||| || ||||| || |||||| |||| ||||||  |||||| |||||||||||||||| |||   || |  ||   ||   | |  || |     |||| |||    |   | | |     | || ||||  | |    || |  || | | |||         ||  | |   
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaa--tgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag

upper sequence: GLYMA07G05230.1 (Glycine max), 5'ss of exon 14
lower sequence: PP1S279_14V6.1 (Physcomitrella patens), 5'ss of exon 4
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagattgatatacctttaagtaacataacagttttacttttacatgtacacactttcaaacataaatgggcacatgcctgattgttaaaacgttccttcttcag----
          | |||||||    ||   | | ||| |||||||||| |||||||||||||||||||| || ||  ||| ||| || || ||  | || ||| || |      | |   || |||     |     |  |   ||   || | |     ||   ||     |      |||| || | || |   | |        ||     
---------CCATGTCTGGAACATACGATGTGAAGGGTGATGTTTACAGCTTTGGAGTTGTCATGTTCGAGCTCATTACTGGGCGCAAGCCTCTGGACAGGGGACACGAgccttttgtttgaagaggggt--tcatcatttcttagaatctgc-tgtatttgtactcgtttcatttgatgcttgctggtaagtgcatgagacgcgcatagcc

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|6666117|gb|AW277576.1|AW277576
EST:     GGAAACCATTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
genomic: GGAAACCATTTGATAGgtgaaagatt ... ccttcttcagCTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
EST: gi|208078027|gb|GD875321.1|GD875321
EST:     TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
genomic: TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagatt ... ccttcttcagCTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
EST: gi|7029604|gb|AW459321.1|AW459321
EST:     TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
genomic: TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagatt ... ccttcttcagCTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
EST: gi|208211697|gb|GE009944.1|GE009944
EST:     TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
genomic: TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagatt ... ccttcttcagCTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
EST: gi|298175534|gb|HO018245.1|HO018245
EST:     TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
genomic: TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagatt ... ccttcttcagCTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
EST: gi|151400859|gb|EV270673.1|EV270673
EST:     TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAG                         CTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT
genomic: TTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagatt ... ccttcttcagCTCAAGGCCGAGGTCTGAGCAGGCTTTGGTTCGATGGGCAACACCTCAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagattgatatacctttaagtaacataacagttttacttttacatgtacacactttcaaacataaatgggcacatgcctgattgttaaaacgttccttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA