Sequence
atgc intronic sequence ATGC exonic sequencegtgagacttgttgtttaatgatgcctctacaacaaatccttttctaatattaaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGTCGTGATGTATACA
Basic information
species | Glycine max |
transcript | GLYMA20G38860.1 |
intron # | 42 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 42
lower sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 6
---------------------------------gtgagacttgttgtt--taatgatgcctctacaaca----aatccttttctaatattaaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGTCGTGATGTATACA
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acttgttcgctgcaccatctactctagcattatataactgttgccaacactcttgctgtcttgcgagcattatattgatgttccaaacataattctgtagGTTGGAAAGGGAAGAGACGTTGGTCTTAATCAGATTGCACTGTTCGAAGGAAAAGTTGCTGGAGGAAATGGTGAGCAAGTGCTCAGCCGGGATATATACA
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 42
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 5
----------------------------------------gtgagacttgttgtttaatgatgcctctacaacaaatccttttctaatattaaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGTCGTGATGTATACA
| | | || | | | || || || |||| | ||| | | | | ||||||| || || || |||||||| || |||||||||||||||||||||||||||||| ||||||| || |||||||||||||| || || || |||| |
ctttggatccctatttggcaattgctttccactgcactaactcaaccgtggt-tgtgctgctgtcttgtgaacactgttgatattaaacgttattctgtagGTTGGCAAAGGTAGGGATGTTGGACTTAATCAGATTGCACTATTTGAAGGAAAAGTTGCTGGTGGAAATGGTGAACAAGTTCTTAGCCGAGACATATATA
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 42
lower sequence: AT3G07160.1 (Arabidopsis thaliana), 3'ss of exon 39
----gtgagacttgttgtttaatgatgcctctacaacaaatccttttcta-at--attaaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGTCGTGATGTATACA
|| || || | || || | |||| | | | || ||| ||||||||| || || || ||||||||||||||||||| || || || |||||||| || ||| ||||||| || |||||||| ||||| ||||| ||||||||||
gtccgtactttttaactctttacaattaaaataataaaaatatatatatgcattaattctgtttacagGTGGGCAAAGGGCGAGATGTTGGGCTCAATCAAATAGCTCTGTTTGAAGGGAAGGTTGCTGGTGGGAATGGTGAACAGGTTCTTAGTCGAGATGTATACA
upper sequence: GLYMA20G38860.1 (Glycine max), 3'ss of exon 42
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 37
gtgagac---ttgttgtttaat-gatgcctctaca----acaaatccttttctaatattaaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGTCGTGATGTATACA
|| |||| | |||| || | ||| |||| | ||| | |||||| ||| ||||||||||||||| ||| |||||||||| |||||||||||||| ||||||||||| |||||| |||||||||| |||||||||||||||||||| || | ||||
gtaagaccactatttgtctatttgatataattacaggaaaaaaaaaaatctctaat-ctaagtttacagGTTGGAAAAGGACGAGATGTTGGACTCAATCAGATTGCTCTATTTGAAGGGAAAGTTGCTGGTGGTAATGGTGAACAAGTTCTCAGTCGAGACATTTACAMapped 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|24205419|gb|BU964672.1|BU964672EST: GAAATATTACACATCATGAATATATTCAG GTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGA
genomic: GAAATATTACACATCATGAATATATTCAGgtgagacttg ... aaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgttgtttaatgatgcctctacaacaaatccttttctaatattaaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGTCGTGATGTATACA
ttctaat putative branch site (score: 2)
aacaaatccttttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagacttgttgtttaatgatgcctctacaacaaatccttttctaatattaaatttacagGTTGGAAAGGGAAGAGATGTTGGGCTCAATCAGATTGCACTATTTGAAGGAAAAGTTTCTGGTGGTAACGGTGAACAAGTTCTCAGTCGTGATGTATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG