Sequence
atgc intronic sequence ATGC exonic sequencegttattttctcagtcaatctcttttgtgcctttacttattatgtatctgtgtcttacgatgtatgagcttcctaagtccttaacccttagttgttgaaaatgggcttccgtcttaaacgaggttcttatcatttgacacaccttacggttttctactttgaattctgatagttgtgattgttgatgtgaacagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTAGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCAA
Basic information
species | Glycine max |
transcript | GLYMA04G00530.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G374574_T02 (Zea mays), 3'ss of exon 2
gttattttctcagtcaatctcttttgtgcctttactta---ttatgtatctgtgtcttacgatgtatgagcttcctaagtccttaacccttagttgttgaaaatgggcttccgtcttaaacgaggttcttatcatttgacacaccttacggttttctactttgaattctgatagttgtgattgttgatgtgaacagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTAGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCAA
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----------------------gtggtgccttccctttgtcttcttcttcctcgttttatcctgtatcatcgctcatcctcactatcatctaaaaatgaaatatgatcagtcatcctctgcatg---catgcccttagccccttaccaaggtg--ctgctaacacatttact--------ttactcgcctgctcagTCTCTACAAGCCCTTAAGAAGATCTCTCTGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCCCTAATGGCTGTTCTATCGTATCTCGACTTCTTCTCCA
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
gttattttctcagtcaatctcttttgtgcctttacttattatgtatctgtgtcttacgatgtatgagcttcctaagtccttaacccttagttgttgaaaatgggcttccgtcttaaacgaggttcttatcatttgacacaccttacggttttctactttgaattctgat----agttgtgattgttgatgtgaacagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTAGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCAA
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-------------------------------------------------------------------------------------gttggctatcataccaatacttgaatcctcgatgctccagctgcttttttaaaaattcttcagggatcacacttgaaatttgattcgtatttatgtatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 1
gttattttctcagtcaatctcttttgtgcctttacttattatgtatctgtgtcttacgatgtatgagcttcctaagtccttaacccttagttgttgaaaatgggcttccgtcttaaacgaggttcttatcatttgacacaccttacggttt-tctactttgaattctgatagttgtgattgttgatgtgaacagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTAGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCAA
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--------------------------------------------------------------------------------------ttcctttgccaaattttattgccat----aatgatgtcaatgttacagaaaatttcccattgcctgcctgcttatagtatttatggtt----tttgtgatggaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caccttacggttttctactttgaattctgatagttgtgattgttgatgtgaacagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTAGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCAA
tttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattttctcagtcaatctcttttgtgcctttacttattatgtatctgtgtcttacgatgtatgagcttcctaagtccttaacccttagttgttgaaaatgggcttccgtcttaaacgaggttcttatcatttgacacaccttacggttttctactttgaattctgatagttgtgattgttgatgtgaacagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTAGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT