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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaacattgtgatgaggaagaaccttttattggatacagaatttcagtttgatattccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG

Basic information

species Glycine max
transcript GLYMA02G31080.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G090689_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------gtaaaaacattgtgatgaggaagaaccttttattggatacagaatttcagtttgatattccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
                                                        || ||| |  |    ||    |  |   ||  ||  ||    |  ||    ||| |     || | |||||| |||||  ||||| |||| ||||| || || ||||| |||||||| ||||||||||| ||||||||||  || | ||  |
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagtgaaagctgtaaactggtccaacatgcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG

upper sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G006753_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------gtaaaaacattgtgatgaggaagaaccttttattggatacagaatttcagtttgatattccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
                                                   | ||| |  |    ||    |  |   ||  ||  ||    |  ||    ||| |     || | |||||| |||||  ||||| |||| ||||| || || ||||| |||||||| ||||||||||| ||||||||||  || | ||  |
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG

upper sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G075485_T02 (Zea mays), 3'ss of exon 5
--------------------------------------------------gtaaaaacattgtgatgaggaagaaccttttattggatacagaatttcagtttgatattccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
                                                   | ||| |  |    ||    |  |   ||  ||  ||    |  ||    ||| |     || | |||||| |||||  ||||| |||| ||||| || || ||||| |||||||| ||||||||||| ||||| ||||  || | ||  |
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctatccagGCTTTTCTGCGCAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGACGAGGCGATTGGTGAAG

upper sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
-----gtaaaaacattgtgatgaggaagaaccttttattgga--tacagaatttcagtttgatat---tccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
      ||  ||   |||              |||| || |   | | | ||     | | || |   | ||||  |||||| |||||||||||||||||||| || ||||| || || || |||||||||||||||||| |||||||||  ||| | || |
gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG

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|193320765|gb|FK283150.1|FK283150
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATT
EST: gi|208184930|gb|GD984944.1|GD984944
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATT
EST: gi|193524564|gb|FK481931.1|FK481931
EST:     AAAATGATTTGAATTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAG                         GCTATTCTGTTCAATG
genomic: AAAATGATTTGA-TTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATG
EST: gi|193495314|gb|FK459336.1|FK459336
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAG                         GCTATTCTGTTCAATG
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATG
EST: gi|208226254|gb|GE026771.1|GE026771
EST:     AAAAATGATTTGATTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATT
genomic: AAAAATGATTTGATTGATCTGTACAAGAAGTGCAAGGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATT
EST: gi|207795714|gb|GD766907.1|GD766907
EST:     AAGTGCAAGGGTAATATGAACAG                         GCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATT
genomic: AAGTGCAAGGGTAATATGAACAGgtaaaaacat ... ccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaggaagaaccttttattggatacagaatttcagtttgatattccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG
                                   gtttgat  putative branch site (score: 5)
                                         tattcccttt  CT-rich tract
                                    tttgatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaacattgtgatgaggaagaaccttttattggatacagaatttcagtttgatattccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT