Sequence
atgc intronic sequence ATGC exonic sequence...tctatgttatttaataattccatcaattttgttttgggcaagtgaggtttgatgaatacttatattgcttgtttgtattatttttttaaaaaaaaattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
Basic information
species | Glycine max |
transcript | GLYMA12G01920.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G01920.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g42240.1 (Oryza sativa), 3'ss of exon 2
tctatgttatttaataattccatcaattttgttttgggca-agtgaggt-ttgat----------gaatacttatattgcttgtttgtattatttttttaaaaaaa------aattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
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-----gtagttcactagtttga-caacatatttttgcacgtactgatgtcttaattgctgcactagaagcttcagagtgttggctgacatcacactgttggttgaattgttctattagGGCAAAATTGCGCCGTGCTAATTTGCATTTCTTGTCTAAGCCGGTCAAAGATGGGACTACTGGAACTGTGATTGTTCTAACAACTCCAGATGCACAACGA
upper sequence: GLYMA12G01920.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G27600.1 (Arabidopsis thaliana), 3'ss of exon 2
---tctatgttatttaataattccatcaattttgttttgggcaagtgaggtttgatgaatacttatat-tgcttgtttgtattatttttttaaaaaaaaattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
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gaatcgttactatacaagagta--gtttgtaaggcgtcaaactagcctatcattacatttggtttggtatactcacaagtttttttttttttgtttcta--tagGACTAAACTACGACGAGCAAATGTAAATTTTCTTTCTGCTCCAATCAAGGACGGAACAACAGGAACAGTGATAGTTCTCACAACTCCTGATGCACAACGT
upper sequence: GLYMA12G01920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0039g01580.t01 (Vitis vinifera), 3'ss of exon 2
--tctatgttatttaataattccatcaattttgttttgggcaagtgaggtttgatgaatacttatattgcttgtttgtattatttttttaaaaaaaaattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
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gagatacattcaattatgatgtctcggttgctgataagaagaagtgtggctccaatgat-cttct-ttaactaactacatactgtcttgatatggtttgtagAACAAAATTGCGTCGGGCAAATGTGAATTTTCTCTCTGCACCTGTTAAGGATGGGACAACGGGGACAGTGATAGTTCTCACGACTCCAGATGCTCAGCGC
upper sequence: GLYMA12G01920.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ20287 (Selaginella moellendorffii), 3'ss of exon 2
tctatgttatttaataattccatcaattttgttttgggcaagtgaggtttgatgaatacttatattgcttgtttgtattatttttttaaaaaaaaattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
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---------------------------------gtaagttcttcgtgctcgatttttatctctcactcactgttgtgtgggttttct------tcgtcagAACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAGGGGCACGACTGGAACAGTGATCGTTCTCACAACACCGGATGCCCAGCGA
upper sequence: GLYMA12G01920.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ23286 (Selaginella moellendorffii), 3'ss of exon 2
tctatgttatttaataattccatcaattttgttttgggcaagtgaggtttgatgaatacttatattgcttgtttgtattatttttttaaaaaaaaattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
| | | || | ||| || | | | |||| | |||| | | || ||| | || || || || || ||||| || | || || || || ||||||||||| || ||||||||||| || |||||||||||
---------------------------------gtaagttcttcgggctcgatttttatctcttactcactgttgtgtgggttttct------tcgtcagAACAAAGCTCTTACGTGCCAACGTACACTTTCTATCATCCCCGATGGTCAGGGGCACGACTGGAACAGTGATCGTTCTCACAACACCGGATGCCCAGCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttgatgaatacttatattgcttgtttgtattatttttttaaaaaaaaattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
gtttgat putative branch site (score: 5)
ttatattgcttgtttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctatgttatttaataattccatcaattttgttttgggcaagtgaggtttgatgaatacttatattgcttgtttgtattatttttttaaaaaaaaattagGGAAAAATTACGCCGAGCAAATGTGCAATTTCTTTCTGCACCAATCAAGGATGGGACTACTGGAACAGTTATAGTTCTCACAACTCCAGATGCCCAGCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - -ccatcaa
- - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - -gcaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt