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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctctttactagtactctcctttggttctttgacatagcatagactatttaaatagggtaagtgtttgacagatttttcattgtatgtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT

Basic information

species Glycine max
transcript GLYMA08G23380.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23380.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
-----------------------------gtgagtctctttactagtactctcctttggttctttgacatagcatagactatttaaatagggtaagtgtttgacagatttttcattgtatgtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
                             |    |||| || |  || |    |||   ||||||    | |    || |  |    | |  ||| |  || |     || |     |   |   |  || | ||||||||||| |||||||||||||| ||||| || ||||| ||||  || ||||| | ||| ||||| || ||||  ||||| ||||||||   ||
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttcttt----ttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT

upper sequence: GLYMA08G23380.3 (Glycine max), 3'ss of exon 3
lower sequence: AT1G80840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtctctttactagtactctcctttggttctttgacatagcatagactatttaaatagggtaagtgtttgacagatttttcattgtatgtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
|| ||  |   |   | |  ||    |||||   |  |  || | |     | || | |    ||  || || || |||| |  |   | | |  || ||| ||||||||||||| || |||||||||||||||||||| || ||||| ||||| || || |  || ||||| || ||||| ||  ||| |||||||||||
gtaagcattcatgaaaatgatcaaacttggtatct--atctatctttagaaactttatt---ttatatggtttactgattgtagaagttgtttc-ttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT

upper sequence: GLYMA08G23380.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 3
------gtgagtctctttactagtactctcctttggttctttgacatagcatagactatttaaatagggtaagtgtttgacagatttttcattgtatgtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
         |  | |   | || |   |  |||||||   || |    |   | || ||    |||  || | || | ||  ||    |   | |||||  ||  || | ||||| ||||||||||| |||||||||||||| |||||||| |||||||| ||||| |  || ||||| || ||||| |||||||||||||| ||||
gtaagtccaaaacccacaaataattggcgactttggtggatt-attctgtgaacaccatccggata--gtgaatgatcgatcgagcaatttctttatgtt-ttacagGTGGTGAAGGATGGATACCAGTGGAGGAAATATGGCCAAAAGGTCACCAGAGACAACCCCTCTCCGAGAGCCTACTTCAAATGCTCTTTTGCTCCTAGCT

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|209706888|gb|BW661498.1|BW661498
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTT                         ATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTTgtgagtctct ... gtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|254342046|gb|GR853183.1|GR853183
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTT                         ATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTTgtgagtctct ... gtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|37995904|gb|CF807493.1|CF807493
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTT                         ATTGTGAAAGATGGATACCAATGGAGGANATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTTgtgagtctct ... gtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|213594145|gb|DB963770.1|DB963770
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTT                         ATTGTGAAAGATGGATACCAATGGAGGGAATATGGACNAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTTgtgagtctct ... gtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|33389342|gb|CA852549.1|CA852549
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTT                         ATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTTgtgagtctct ... gtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|192300003|gb|FG991835.1|FG991835
EST:     CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTT                         ATTGTGAAAGATGGATACCAATGGAGGAAGTATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTTgtgagtctct ... gtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|254318274|gb|GR832442.1|GR832442
EST:     CAAAAATTTCAAGAGTTTATGTCACGACTGAATCATCTGATACTAGCCTT                         ATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTTgtgagtctct ... gtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|11411497|gb|BF423508.1|BF423508
EST:     CAGAGATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTT                         ATTGTGATAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATGTCAGGACTGAATCATCTGATACTAGCCTTgtgagtctct ... gtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactatttaaatagggtaagtgtttgacagatttttcattgtatgtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
                      gtttgac  putative branch site (score: 4)
                               atttttcattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctctttactagtactctcctttggttctttgacatagcatagactatttaaatagggtaagtgtttgacagatttttcattgtatgtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT