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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtctgactgggagtttgggactaactaatggtgtcatttatgttcttcactaacgctttctgcattgatgatgatgatgagtaccattctaccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG

Basic information

species Glycine max
transcript GLYMA01G35190.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 11
gtgagtgtctgactgggagtttgggactaactaatggtgtcatttatgttcttcactaacgctttctgcattgatgatgatgatgagtaccattctaccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG
                  || ||  |   | |||   |   |   ||  | ||  || |   ||| |  ||| |||  ||||        ||       || |    | |   ||  || ||  ||  |||| ||||||||||||||||| |||||||||||||| ||  | || | |||||| || || ||  ||||
------------------gtatgaaa---aataaaactaaaaaa-atactatttgcttagtgtttgtctattcatg--gatggaccaactcaactcgtaatctgacatttcttcacctcgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGCTGTTGACACTCCATCCTCTCTTTCCTGGAACCAG

upper sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 10
gtgagtgtctgactgggagtttgggactaactaatggtgtcatttatgttcttcactaacgctttctgcattgatgatgatgatgagtaccattctaccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG
                  || ||  |  ||  || ||  |  | | || |      ||  | ||| |   || |||         | |    || || | |    ||| ||  ||  |  ||  ||  |||| ||||||||||||||||| |||||||||||| | ||  | || | |||||| || || ||  | ||
------------------gtatgaaa--aataaaaggcttactatttgct------tagtgttttgtcttttcatgggtggaccaactcagcttgtaacctgacatttctt--caccttgccatctcatagATATGTGGGCAATGGGTGCCATAATGGCTGAGTTGTTGACACTCCATCCTCTCTTTCCTGGAACTAG

upper sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 7
gtgagtgtctgactgggagtttgggactaactaatggtgtcatttatgttcttcactaacgctttctgcattgatgatgatgatgagtaccattctaccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG
|| ||| | |   ||| |    | |||| |  |||       ||||||   ||    ||   | ||   |||  ||    |          |  ||   ||||| |||     |||||   |||  || ||| |||||||||||||||||||| ||||||||  | ||  |||| |||||||| || |||||  | ||
gtcagtatatagttggaaa---gagactga--aat-------tttatgaagtttgaaaaaa-tatccatatttttgtctgtag--------acactgaaattttatttc----cattttttccc--tccagATATGTGGGCAATGGGTGCTATCATGGCTGAATTGTTTACTCTCCGTCCTCTCTTTCCAGGATCGAG

upper sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 7
gtgagtgtctgactgggagtttgggactaactaatggtgtcatttatgttcttcactaacgctttctgcattgatgatgatgatgagtaccattctaccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG
                             | |  || | ||      |   ||       |  |     ||  ||  | ||  || |   |  |     |  |  || | ||| | ||     | ||  |||  |||||||| |||| || ||||||||||| |||||| | |||||||| |||||||| ||||| ||
--------------------------tgtatttgtgctttcgcagcagcagttagtcgttgtatctgttat--atactcattctgtgcctctcttctggaagtacttaagtaaaaatttt---catttcagATGTGTGGGCAGTGGGAGCAATAATGGCTGAACTTTTCACCCTTCGTCCACTTTTCCCTGGTGCAAG

upper sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ22662 (Selaginella moellendorffii), 3'ss of exon 5
gtgagtgtctgactgggagtttgggactaactaatggtgtcatttat-gttcttcactaacgctttctgcattgatgatgatgatgagtaccattc-taccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG
                                  | |  || ||| | |||| |  |  |    || ||||||      | |   | |  ||     |   | |    |  |     |    | |     | ||||||||||||||||||||||| |||||||||||||||  |||  |                     
---------------------------------gtagcttcttttgttgttcgttgcgta-atcttatgcattacctcagGTACCGTGCCCCGGAGGTGTTACTGCAGTCGTCTCTGTACAACTCTGCGGTCGACATGTGGGCAATGGGTGCTATCATGGCTGAGCTTTTCAATCTCAGG--------------------

upper sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ11811 (Selaginella moellendorffii), 3'ss of exon 5
gtgagtgtctgactgggagtttgggactaactaatggtgtcatttat-gttcttcactaacgctttctgcattgatgatgatgatgagtaccattc-taccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG
                                  | |  || ||| | |||| |  |  |    || ||| ||      | |   | |  ||     |   | |    |  |     |    | |     | ||||||||||||||||||||||| |||||||||||||||  |||  |                     
---------------------------------gtagcttcttttgttgttcgttgcgta-atcttatgctttacctcagGTACCGTGCTCCGGAGGTGTTACTGCAGTCGTCTCTGTACAACTCTGCGGTCGACATGTGGGCAATGGGTGCTATCATGGCTGAGCTTTTCAATCTCAGG--------------------

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|7589585|gb|AW705356.1|AW705356
EST:     TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTG                         ACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
genomic: TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTGgtgagtgtct ... ccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
EST: gi|254336468|gb|GR842647.1|GR842647
EST:     TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTG                         ACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
genomic: TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTGgtgagtgtct ... ccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
EST: gi|254345622|gb|GR855958.1|GR855958
EST:     TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTG                         ACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
genomic: TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTGgtgagtgtct ... ccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
EST: gi|14205773|gb|BG839451.1|BG839451
EST:     TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTG                         ACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
genomic: TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTGgtgagtgtct ... ccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
EST: gi|192299757|gb|FG990052.1|FG990052
EST:     TCGTGCTCCTGAGGTGCTGCCTCAGTCTTATCTGTATACCTCTAAAGTTG                         ACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
genomic: TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTGgtgagtgtct ... ccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
EST: gi|26048711|gb|CA785164.1|CA785164
EST:     TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTG                         ACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
genomic: TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTGgtgagtgtct ... ccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
EST: gi|22522544|gb|BU081355.1|BU081355
EST:     TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTG                         ACATGTGGGCAATGAGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
genomic: TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTGgtgagtgtct ... ccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
EST: gi|298163466|gb|HO012199.1|HO012199
EST:     TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTG                         ACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC
genomic: TCGTGCTCCTGAGGTGCTGCTTCAGTCTTATCTGTATACCTCTAAAGTTGgtgagtgtct ... ccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatgatgagtaccattctaccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG
                               tattaac  putative branch site (score: 1)
                                     catttcccccccttct  CT-rich tract
                       attttgtttattaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtctgactgggagtttgggactaactaatggtgtcatttatgttcttcactaacgctttctgcattgatgatgatgatgagtaccattctaccattttgtttattaacatttcccccccttctagACATGTGGGCAATGGGTGCTATAATGGCTGAGCTTTTCTCTCTTCGTCCTCTTTTCCCAGGTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT