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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcacatcttcattctcattccgcgtttccctttttctcactttttttttttttcaatttgaagctaaaatgtgtataaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG

Basic information

species Glycine max
transcript GLYMA03G30880.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g39444.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------gtctcacatcttcattctcat--tccgcgtttccctttttctcactttttttttttttcaatttgaagctaaaatgtgtataaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG
                                                      |||||  | |  |  ||||  |    |   || || |       ||||||   |  | |  |     |||         |   ||||||||| ||||||||||||||||| || ||  | ||||||||||||||||| || || || || || ||||| || |
gtgaggctccggttcttctccacttcgttctgtcccgtttcgtttccctgtgtgtcttccctttgctgatccgtatggtgcaaattttcccccgcgaatttttttggtgcggatttggggcgtggggggtttcgctgcagGTTTCTGATGAAGCTGAACAACGAGACGGTCACCATCGAGCTCAAGAACGGCACCGTCGTCCACGGAACCATCACCG

upper sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G027571_T02 (Zea mays), 3'ss of exon 1
----------------------------------gtctcacatcttcattctcattccgcgtttccctttttctcactttttttttttttcaatttgaagctaaaatgtgtataaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG
                                  |  |    |   | ||  | |||| ||   | |  |||   ||    ||    | |   ||||  ||| |  |  ||      | |   |||||| || |||||||||||||| || || ||  | ||||||||||||||||| || ||||| || |||||||| || |
gtaacgcccccccgtattcgttcgcccattgttagggttggcttccctttaccgttcctcgccgctccgtttgctacgaacttcgcctat---tttggtgctcatttcggtgcgcttc-gccgcagGTTCCTTATGAAGCTGAACAATGAGACGGTCACCATCGAGCTCAAGAACGGCACGGTTGTACACGGCACCATCACCG

upper sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 1
---------------------gtctcacatcttcattctcattccgcgtttccct----ttttctcactttttttttttttcaa----tttgaagctaaaatgtgtat---aaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG
                        | |  |||||  | | |||     || |       ||||   | || | ||| ||||||     || || | |  | |  ||||    |   |    ||||||| | |||||  ||||||||||||| |||||||||||||| |||||||||||  |||||||||| |||||||| |
gtatggtttctactcggattctctttatttcttcggtttaattggaatttgcttcgaaattttgagatttctctttgttttcatgctcttcgatgtttgatttcgtatctggattttttcgcagGTTTTTGATGAAATTGAACAACGAAACAGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG

upper sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 1
gtctcacatcttcattctcattccgcgtttccctttttctcactttttttttttttcaatttgaagctaaaatgtgtataaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG
        ||| | || |  ||| |  |||| ||| || |||   || |  ||    | | |  | |||   ||  ||  ||| |    ||||||| | |||||||| |||||||| || || ||||| |||||||||||||| || ||||||||||||||||| ||||
-------gtctgc-ttatttttcagtttttctcttgttttca---ttctcattaactattgttgacctagcttg-atacgaaattt---cagGTTTTTGATGAAGCTCAACAACGAGACTGTGTCAATTGAGCTCAAGAACGGTACCGTTGTTCATGGCACCATCACAG

upper sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 3
gtctcacatcttcattctcattccgcgtttccctttttctcactttttttttttttcaatttgaagctaaaatgtgtataaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG
|| | |  |     |  | |         |    |  ||||  ||| ||| ||||    | | ||  |   ||   | ||       ||||||||||| |||||| |||||||||||||||| || |||||||||||||| ||||| || |||||||||||||| ||||
gtttgatcttcaattaattaccatatacatatactaatctcgatttatttattttgttttgttaaattcttata-atttagtctaaaaacagGTTTCTGATGAAGTTGAACAACGAAACCGTGTCTATCGAGCTCAAGAATGGAACCGTGGTTCATGGCACCATAACAG

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|298174427|gb|HO014572.1|HO014572
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|9900352|gb|BE609320.1|BE609320
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|13480558|gb|BG509901.1|BG509901
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|254323967|gb|GR836199.1|GR836199
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|12773904|gb|BG238831.1|BG238831
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|8827595|gb|BE211325.1|BE211325
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|4437132|gb|AI522997.1|AI522997
EST:     GTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: GTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|298198717|gb|HO042080.1|HO042080
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|27424994|gb|CA936514.1|CA936514
EST:     CTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: CTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|298193977|gb|HO040625.1|HO040625
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCACATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|15285034|gb|BI468925.1|BI468925
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|254334206|gb|GR849124.1|GR849124
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|7925936|gb|AW831962.1|AW831962
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|19269395|gb|BM885651.1|BM885651
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|254323968|gb|GR836200.1|GR836200
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGC-TGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|6846635|gb|AW348925.1|AW348925
EST:     CCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGANNNCGTTTCAATCGAGCTCAAGAACGG
genomic: CCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|15815172|gb|BI787447.1|BI787447
EST:     CGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: CGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|254334205|gb|GR849123.1|GR849123
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|298186306|gb|HO036939.1|HO036939
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGCTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|31468972|gb|CD411000.1|CD411000
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|298172347|gb|HO019387.1|HO019387
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|6482740|gb|AW201964.1|AW201964
EST:     AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: AAAACCCTGCCGTCAGTCACCGTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
EST: gi|31473716|gb|CD415744.1|CD415744
EST:     GTCTTCTCTGCCGCCATGAAGCTTGTCAG                         GTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG
genomic: GTCTTCTCTGCCGCCATGAAGCTTGTCAGgtctcacatc ... actggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcactttttttttttttcaatttgaagctaaaatgtgtataaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG
      tttttttttttttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcacatcttcattctcattccgcgtttccctttttctcactttttttttttttcaatttgaagctaaaatgtgtataaaactggaacagGTTTCTCATGAAGCTGAACAACGAAACCGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC