Sequence
atgc intronic sequence ATGC exonic sequence...gtatggcatgttcttgtgcatctactgtgagatagttgttttaacctttctatgttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG
Basic information
species | Glycine max |
transcript | GLYMA06G06310.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G166035_T02 (Zea mays), 3'ss of exon 4
-----gtatggcatgttcttgtgcatctactgtgagatagttgttttaacctttctatg-ttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG
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gctgaatcagaatcagtttctcaaatcgtttgtcaggattccaatctaatcgcattacacttcaacaatttt---atgatgttttccccatcttga---cctgcagCAATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGGCAAAGAATTGAGGATGCAGGGGGCTTTGTTATGTGGGCTG
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G829894_T01 (Zea mays), 3'ss of exon 3
-------gtatggcatgttcttgtgcatctactgtgagatagttgttttaacctttctatgttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG
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ttgtgacgaatggataaactgaatatcaggattccaagctaaccacgtt---ccacttgtattcgatattttttg--ttatgttttccccatctcggag--ctgcagCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 4
gtatggcatgttcttgtgcatctactgtgagatagttgttttaacctttcta----tgttgaat-atttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG
|| || | || | | | | | | | | | ||| ||| || | ||| || | || | || | || | | | || || | ||| ||||||||||| |||||||||||||| |||||||||||| |||| | |||||||| || ||||| ||||| |||||||| |
ctactgc-taagctag-gagttgattctacggctgatatttcaacattggtgacaccgtttaaccactttcctaacttgatgcattc---tgcttctttttgcagCTATTGCTGTTTCAAAGGATCACAAGCCTGATCAAACTGATGAGCGGCAGCGTATTGAAGATGCTGGAGGTTTTGTGATGTGGGCAG
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 5
----gtatggcatgttcttgtgcatctactgtgagatagttgttttaa-cctttctatgttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG
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acatacttataatcacatgatagcccttgttcatgaaatttgcaataagtcgctctgttttgtatggt-act-aatttgatatttt---tttttgtttgtcaaagCTATTGCTGTATCCCGAGATCACAAGCCTGATCAAAGTGACGAGCGCCAAAGAATTGAGGATGCAGGAGGATTTGTCATGTGGGCTG
upper sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 5
gtatggcatgttcttgtgcatctactgtgagatagttgttttaacctttctatg--ttgaatatttgctgaatattattcttccaa-ttgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG
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-gatgaattaaagatcttc-tctatggagaatttgcttcgtctagtgttcactggtttcagtgtttgatca-tctgatgaaaacatcttgtaatttcctccagCCATTGCTGTTTCTCGAGATCACAAGCCAGACCAAACTGATGAGCGGCAGCGTATTGAGGATGCTGGAGGGTTTGTGATGTGGGCTGMapped 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|192305900|gb|FG995786.1|FG995786EST: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG CCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAA
EST:
gi|14260019|gb|BG882927.1|BG882927EST: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATG CCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAA
genomic: TGTTGCAAATGTTGGGGATTCCAGAGCTGTTATATGCAGGGGTGGTAATGgtaagggtgt ... tttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttctatgttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG
tttcctct CT-rich tract
tatgttgaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggcatgttcttgtgcatctactgtgagatagttgttttaacctttctatgttgaatatttgctgaatattattcttccaattgtggtttcctctagCCATTGCTGTTTCTCGAGATCACAAGCCTGACCAAACTGATGAGAGGCAAAGGATTGAAGAAGCAGGAGGCTTTGTTATGTGGGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - -gcatgtt
- - - - - - cttgtgc
- - - - - - - - - - tctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa