Sequence
atgc intronic sequence ATGC exonic sequence...atatattttagcctaatctttactgttatagtaatttttttggtttgatattcaagttattggcaacaaaggcttattggagcacatgtttcctgtgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGGGTTATTCATCAAAGAAGTCAAAGACAACAATTGGACAGT
Basic information
species | Glycine max |
transcript | GLYMA16G24450.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G36270.1 (Arabidopsis thaliana), 3'ss of exon 4
atatattttagcctaatctttactgttatagtaatttttttggtttgatattcaagttattggcaacaaaggcttattggagcacatgtttcctg--tgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGGGTTATTCATCAAAGAAGTCAAAGACAACAATTGGACAGT
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gtatattt---cctattatagagtgt-gtagtgcttttcccttaccgaggctttgtatgttgttaat---gacatggtgtcttctttttttccaacttgaagATGATGGCGGTGGAATGGATCCCGATGGGCTCAGAAAATGCATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACGACGATTGGACAGT
upper sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G36280.1 (Arabidopsis thaliana), 3'ss of exon 4
atatattttagcctaatctttactgttatagtaatttttttggtttgatattcaagttattggcaacaaa--ggcttattggagcacatgtttcctgtgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGGGTTATTCATCAAAGAAGTCAAAGACAACAATTGGACAGT
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gtacatttcctttgaat------gactgtggtgcttttgcctaaccaaggcttgggatgttgttattgatatggtttctctcctttctttttgaacttgaagATGATGGTGGTGGGATGGATCCCGCTGGGCTCAGAAAATGCATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACAACGATTGGACAGT
upper sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G36290.1 (Arabidopsis thaliana), 3'ss of exon 4
atatattttagcctaatctttactgttatagtaatttttttggtttga----tattcaagttattggcaacaaaggcttattggagcacatgtttcctgtgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGGGTTATTCATCAAAGAAGTCAAAGACAACAATTGGACAGT
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-------gtacactgcctttgaatgtattggtggtgcttttgcgtaaaggagtttttgaatcttgtgcatgacattatccttcttttgtttttttcacttgaagATAATGGTGGTGGGATGGATCCTAATGGGATCAGAAAATGCATGAGCTTAGGCTACTCGTCAAAGAAGTCTAATACGACAATTGGACAAT
upper sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g02740.t01 (Vitis vinifera), 3'ss of exon 4
atatattttagcctaatctttactgttatagtaatttttttggtttgatattcaagttattggcaacaaaggcttattggagcacatgtttcctgtgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGGGTTATTCATCAAAGAAGTCAAAGACAACAATTGGACAGT
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--------------gtatggtattaatatatgaccagatgtggcttcttgcatcattttttaataaatgataagtgggcaactatggatgttttgtacagATGATGGAGGTGGAATGGATCCTGAATCTATTCGGAAATGCATGAGCTTGGGTTACTCTTCAAAGAAGTCGAACACAACAATTGGACAATMapped 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|208049587|gb|GD844892.1|GD844892EST: TGATAAGCTTGATGTCAAGAAGGATAATTCACCAGCATTATGTTTTCTAG ATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGG
genomic: TGATAAGTTTGATGTCAAGAAGGATAATTCACCAGCATTATGTTTTCTAGgtatccaatt ... tcctgtgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatattcaagttattggcaacaaaggcttattggagcacatgtttcctgtgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGGGTTATTCATCAAAGAAGTCAAAGACAACAATTGGACAGT
gtttgat putative branch site (score: 5)
tgtttcct putative PPT
aagttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatattttagcctaatctttactgttatagtaatttttttggtttgatattcaagttattggcaacaaaggcttattggagcacatgtttcctgtgcagATGATGGTGGTGGAATGAACCCTAATGCAATTCGAAAATGCATGAGCTTGGGTTATTCATCAAAGAAGTCAAAGACAACAATTGGACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatgt