Sequence
atgc intronic sequence ATGC exonic sequencegcacgtaaaattgcttcttgtgtgttttcatgtccttgttctggcaaaattagtttacttgttttcactatactgtttcatatagttcaccaactctagttctaaataaatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
Basic information
species | Glycine max |
transcript | GLYMA16G04560.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 2
gcacgtaaaattgcttcttgtgtgttttcatgtccttgttctggcaaaattagtttacttgttttcactatactgtttcatatagt-tcaccaactctagttctaaataaatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
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---------------------acttaaccaggatcagtattttataaggttcatctgggctttccccc----ctatccgaaacagtatgttcaacttttgagt--aacaagcagtttgtggt--tgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGATTTAGGGTTCAACATGATAATGCTAGGGGACCTATGAAGGGTGGAATCA
upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 1
gcacgtaaaattgcttcttgtgtgttttcatgtccttgttctggcaaaattagtttacttgttttcactatactgtttcatatagttcaccaactctagttctaaataaatgtttc--acaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
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----------------------------ccgacccgcttttttgtggatccagtt-acttcaatccggt-tgctgaattatataaccggaacaaaccaatttaaatcaaccggttctggtatttttgtagGTGGAATGTACCATACCGAAAGACGATGGTACACTAGCATCATTCGTTGGGTTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 1
gcacgtaaaattgcttcttgtgtgttttcatgtccttgttctggcaaaattagtttacttgttttcactatactgtttcatatagttcaccaactctagttctaaataaatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
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------------gttcgatgttttcctctgttttcttcttccatctataacag---atctgcagaaccgatccggttcaagatcatttg--aac---ggaactaaccaactatt----------gcagGTGGAATGTACCATACCAAAAGACGATGGAACTCTAGCATCCTTTGTTGGATTCAGAGTTCAACACGACAATGCAAGAGGTCCCATGAAAGGTGGAATCA
upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 3
gcacgtaaaattgcttcttgtgtgttttcatgtccttgttctggcaaaattagtttacttgttttcactatactgtttcatatagttcaccaactctagttctaaataaatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
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-------------------gtggtttctaatgatat-------gctcagttttctcatccatgataaccgtatgatttaccattttttgactatgctcttttcacttc--ttttgaacaaaattgcagGTTGAGTGCACCATACCCAAAGACGATGGTACTTTGGCATCATTTGTTGGATTCAGGGTTCAACATGACAATGCTAGAGGCCCCATGAAGGGAGGGATCAMapped 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|4397421|gb|AI496418.1|AI496418EST: TGGATTCAAAGCTTGAGAAAAGTTTGCTGATTCCATTCAGGGAAATCAAG GTTGAATGTACCATACCTAAAGATGATGGCACGTTGCAATCTTATGTTGGG
genomic: TGGATTCAAAGCTTGAGAAAAGTTTACTGATTCCATTCAGGGAAATCAAGgcacgtaaaa ... aataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGG
EST:
gi|10847674|gb|BF070321.1|BF070321EST: TGGATTCAAAGCTTGAGAAAAGTTTACTGATTCCATTCAGGGAAATCAAG GTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGG
genomic: TGGATTCAAAGCTTGAGAAAAGTTTACTGATTCCATTCAGGGAAATCAAGgcacgtaaaa ... aataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttcatatagttcaccaactctagttctaaataaatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
ttctaaa putative branch site (score: 2)
taaataaatgtttcac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcacgtaaaattgcttcttgtgtgttttcatgtccttgttctggcaaaattagtttacttgttttcactatactgtttcatatagttcaccaactctagttctaaataaatgtttcacaataatgcagGTTGAATGTACCATACCTAAAGATGATGGCACCTTGCAATCTTATGTAGGGTTCAGGGTTCAACATGATAATGCCAGAGGCCCCATGAAAGGAGGAATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA