Sequence
atgc intronic sequence ATGC exonic sequencegtactcactttgtgtgagtcattctgatttcaagatatagcatgtctatggatttgcatattttcttctgctggcattcatgcacaagaaaaggaggaaagaaacaatttaatagaagtaataattctgagtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
Basic information
species | Glycine max |
transcript | GLYMA13G43000.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g53700.1 (Oryza sativa), 3'ss of exon 6
-----gtactcactttgtgtgagtcattctgatttcaagatatagcatgtctatggatttgcatattttcttctgctggcattc--atgcacaagaaaaggaggaaagaaacaatttaatagaagta---ataattctga-gtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
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gtattgttggcaaacatcaaatttaaccattattcagagacaaaactcaactatgg---tataccttttatgtagtttactgtctagtagactgccttatatgttcaccatttctttatacgcaatatggatggtcttgttattttgcagATGCTCATGGGAGGAGGTGGTTCTTTCTCTGCTGGTGGTCCTGGGAAGGGCATGCATTCTCGATTGT
upper sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G005036_T01 (Zea mays), 3'ss of exon 6
gtactcactttgtgtgagtcattctgatttcaagatatagca-tgtctatggatttgcatattttcttctgctggcattcatgcacaagaaaaggaggaaagaaacaatttaatagaagtaataattctgagtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
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-----------------------gccatttct---tctagcggtgttaaaaaacaatcacatgtgctgttgcatatgctaatcta-----atagtgcttcaaaggtatgttgat--------caatttgttgtc-tgtagATGCTCATGGGAGGAGGAGGGTCCTTCTCTGCTGGTGGGCCTGGAAAGGGAATGCATTCTCGATTGT
upper sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G16480.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactcactttgtgtgagtcattctgatttcaagatatagcatgtctatggatttgcatattttcttctgctggcattcatgcacaagaaaaggaggaaagaaacaatttaatagaagtaataattctgagtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
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---------------------------------------------------------gtgcctgactcaaatacattacttgatctttcaaacg--caaagacttaattgtgtaaaatc--caattctta-----tcagATGCTTATGGGAGGAGGTGGCTCATTTTCTGCGGGAGGCCCTGGAAAAGGAATGCACTCTTGGCTCT
upper sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G51980.2 (Arabidopsis thaliana), 3'ss of exon 6
gtactcactttgtgtgagtcattctgatttcaagatatagcatgtctatggatttgcatattttcttctgctggcattcatgcacaagaaaaggaggaaagaaacaatttaatagaagtaataattctgagtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
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---------------gtgtctaattgaattttactttttggttgctt-taacttt---cacttgtttcgatcaaattttttttactggcgaaaaagtaataaaatg---taatctaattgcta------------ttagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGAGGTCCTGGAAAAGGAATGCACTCGTGGCTTT
upper sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g03200.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------gtactcactttgtgtgagtcattctgatttcaagatatagcatgtctatggatttgcatattttcttctgctggcattcatgcacaagaaaaggaggaaagaaacaatttaatagaagtaataattctga--gtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
| || || | | | || ||| | || |||| || | ||| || | |||| | | | | |||| | | | || | | | ||| || | ||| ||| ||||||||||||||||||||||| || |||||||| || || ||||||||||| ||||| ||| | || |
gtgctgcatttgatcttttcttcttaaagagattctgctatctctctctctctctctctc-tctctctctata-tatatatatatatatatatatatatatatattcatattccctcttttcattcatccaccatgttttccttttttgcattaagaaatgtgatagtcccgcagATGCTTATGGGAGGAGGTGGCTCATTCTCTGCGGGGGGCCCTGGAAAAGGAATGCACTCACGACTAT
upper sequence: GLYMA13G43000.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv10s0003g03230.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------gtactcactttgtgtgagtcattctgatttca-agatata-gcatgtctatggatttgcatattt-tcttctgctggcattcatgcacaagaaaaggaggaaagaaacaatttaatagaagtaataattctgagtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
||| || | | | || ||| | | | ||||| || | ||| || | |||| | | || | ||||||| ||| | | |||| | | || ||| | ||| ||||| ||||||||||||||||| || |||||| | || || ||||||||||| ||||| ||| | || |
gtgctgcatttgatcttttcttcttaaagagattctgctatttggaaatctctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatattccctcttttcattcatccacc----atgttttccttttttgcattaagaaatgtgatagtcctg-------cagATACTTATGGGAGGAGGTGGCTCATTCTCTACGGGGGGCCCTGGAAAAGGAATGCACTCACGACTATMapped 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|8402432|gb|BE058066.1|BE058066EST: CTGGTGGCTGGAAAAAAGAGAAAGAAGCTATTGCTTTGACTATTCTACAG ATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGG
genomic: CTGGTGGCTGGAAAAAAGAGAAAGAAGCTATTGCTTTGACTATTCTACAGgtactcactt ... agtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGG
EST:
gi|18041237|gb|BM309531.1|BM309531EST: CTGGTGGCTGGAAAAAAGAGAAAGAAGCTATTGCTTTGACTATTCTACAG ATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAAGG
genomic: CTGGTGGCTGGAAAAAAGAGAAAGAAGCTATTGCTTTGACTATTCTACAGgtactcactt ... agtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagaaaaggaggaaagaaacaatttaatagaagtaataattctgagtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
atttaat putative branch site (score: 4)
aaagaaacaatttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcactttgtgtgagtcattctgatttcaagatatagcatgtctatggatttgcatattttcttctgctggcattcatgcacaagaaaaggaggaaagaaacaatttaatagaagtaataattctgagtcgttcagATGCTTATGGGAGGAGGTGGGTCGTTCTCTGCTGGAGGGCCTGGAAAAGGGATGCATTCAAGGCTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG