Sequence
atgc intronic sequence ATGC exonic sequence...tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
Basic information
species | Glycine max |
transcript | GLYMA01G36880.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactat---ttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
| || || ||| | || || | | || |||| || | | ||| || | || | | | ||||||| | | | ||||||||||||| ||||||||||| || || || || |||||||||||||| ||||| || |||||||| || |||||||||||||| |
gtattcatcaatcattctccctcctttttttgatatctgattcatttgattctgattgtgccata-tatgaattgggatccatacatactaaaaatgttgtatacatttccattggaacagGATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAG------------
upper sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------------------------------------------------------------------tattatttattatgaagtttggtt--aacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtat-ttgtatattta---aaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
| || | | || | | | | || |||| | ||| ||||| ||||| | || || || | ||| || ||||| ||| | ||||||||||||| ||||||||||| || || || ||||||||||||||||| ||||| || ||||||||| || | |||||||| || |
gtataatgttccttccttagattgaatcatattctgtgttctgtgaattacaagcttcaaaattgtcttctctattgattgatgagaccaaagcttgtggcaatacatgaatcgatccataatttttttttggtgttatgaggatttgtggagct-ttgtatctcattgaatcttgtaaattcatgtggaacagGATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAATGGAGCCACTGTGAATCTTGGGCTATGGGATACCGCAG------------
upper sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G51300.1 (Arabidopsis thaliana), 3'ss of exon 1
tattatttattatgaagtttggttaacgttttttgttttgtt-ttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
|||| | | | | | || | |||| |||||| || || | | | | | | || | ||| ||||| || || |||||||||||||| || ||||| || |||||||| || ||||| || || ||||| |||| ||||||||| || |||||||| ||||| |
-gttatgtcccaattattct--ttcatgtttcttgtttcattaccacaacaacaacatatctca-tgtt---tcttgtttcttttgtggatata----cagGATTATGTGCCTACCGTTTTCGATAATTTCAGTGCCAATGTTGTGGTTAATGGAAGCACTGTGAATCTTGGATTGTGGGACACTGCAG------------
upper sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 2
---tattatttattatgaagtttgg----ttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
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gaaaagaatcttccaaaaaaattaaggacttcggatcattcttttttttctttgataggcaaaggacttattgttttatt--tttgaat-----tattgggaaacagGATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTG------------
upper sequence: GLYMA01G36880.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ09765 (Selaginella moellendorffii), 3'ss of exon 1
tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtat-atttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
|| ||| || || | || || | | | | | ||| | | || || | |||||||||| || || ||||||||||| || |||||||| |||||||||||| |||| | || ||| || || || | ||||| |||||||
----------------------------------gtgagatttcgttttgttctttccttt--ttctctaactctcttgggctgggatcgttcatcaacagGATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG------------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|13180797|gb|BG352137.1|BG352137EST: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACC GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAAT
EST:
gi|12688223|gb|BG154559.1|BG154559EST: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCTCC GATGTATGTGACGACTGTTTTTGACGATTTAAGCGCAAATGTGGTTGTCAA
genomic: TGGGCAAAACCTGTTTGCTTATTTCCTACACCAGCAACACTTTTCCCACCgttagtactt ... ttaaaaacagGAT-TATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
attacgttgtatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattatttattatgaagtttggttaacgttttttgttttgttttgtaatgagcatttggttaactatttgattacgttgtatttgtatatttaaaaacagGATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGGTAATGCTGCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC