Sequence
atgc intronic sequence ATGC exonic sequencegtagttaattatataacatacgctttttaaaattatttttttatttgattcatgtcttcaagacattttttttaattgaatccttatgtttatatatatagtacttacttttgaagggttttctttgtgcagGTTATTTTAATCTCATTTTCAACTTGGCTTGCATGGTTTTTAGCTGGAAGATTTCATGCTTACCCCAAGTCTTGGATACCATCTTCCATGGATAGCTTTC
Basic information
species | Glycine max |
transcript | GLYMA19G32190.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G32190.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g46940.1 (Oryza sativa), 3'ss of exon 2
gtagttaattatataacatacgctttttaaaattatttttttatttgattcatgtcttcaagacattttttttaattgaatccttatgtttatatatatagtacttacttttgaagggttttctttgtgc----agGTTATTTTAATCTCATTTTCAACTTGGCTTGCATGGTTTTTAGCTGGAAGATTTCATGCTTACCCCAAGTCTTGGATACCATCTTCCATGGATAGCTTTC
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---------------------------------------------------------gtaagttcagtttcatcgtggtaattcaacggatat-catttctta-tcaattctaaatagtcttcttcatcctttcagGTCATCATTCTTTCTTTGCTTACTTGGCTTGCTTGGTTCTTAGCTGGGAGGCTTCATGGTTACCCTAACTCATGGATACCATCTTCCATGGATAGCTTTC
upper sequence: GLYMA19G32190.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143512_T01 (Zea mays), 3'ss of exon 2
gtagttaattatataacatacgctttttaaaattatttttttatttgattcatgtcttcaagacattttttttaattgaatccttatgtttatatatat-agtacttacttttgaagggttttctttgtgcagGTTATTTTAATCTCATTTTCAACTTGGCTTGCATGGTTTTTAGCTGGAAGATTTCATGCTTACCCCAAGTCTTGGATACCATCTTCCATGGATAGCTTTC
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---------------------------------------------------gtatgctcagttacgtttttgtaataaaatcaatgggggtaaacttatcaatgctgaat---aatcttccccatgtttgcagGTTATCGTTCTCTCTTTGCTTACTTGGCTTGTGTGGTTCTTAGCTGGGAGATTCCATGGTTACCCATACTCATGGATACCATCTTCCATGGATAGCTTTC
upper sequence: GLYMA19G32190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 3'ss of exon 2
----gtagttaat-tatataacatacgctttttaaaattatttttttatttgattcatgtcttcaagacattttttttaattgaatccttatgtttatata-tatagtacttacttttgaagggttttctttgtgcagGTTATTTTAATCTCATTTTCAACTTGGCTTGCATGGTTTTTAGCTGGAAGATTTCATGCTTACCCCAAGTCTTGGATACCATCTTCCATGGATAGCTTTC
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gtaaacatctaatatacatttc-tcctctccttcagtttcttttgttttctaaattgagtgataagtac-tataaattatgtgaaaatgaatgataatttaatccaggcctttgcctacaactgcctatcttttgcagGTTATTATCCTCTCATTTTCCACTTGGCTTGCCTGGTTTTTAGCTGGAAAGTTCAATGGATATCCGAAATCTTGGATACCGACTTCAATGGATGGTTTTC
upper sequence: GLYMA19G32190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03630.t01 (Vitis vinifera), 3'ss of exon 8
gtagttaattatataacatacgctttttaaaattatttttttatttgattcatgtcttcaagacattttttttaattgaatccttatgtttatatatatagtacttacttttgaagggttttctttgtgcagGTTATTTTAATCTCATTTTCAACTTGGCTTGCATGGTTTTTAGCTGGAAGATTTCATGCTTACCCCAAGTCTTGGATACCATCTTCCATGGATAGCTTTC
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-------------------------gtaaacattaaaatgccttctcattggtttccttatg----tattctaaatagag---tgataatttggtttcaggcctttgctgacaattgtaaatcttt-tgcagGTCATTGTCCTTTCATTGTCAACTTTTCTTGCCTGGTTTTTAGCTGGAAAGTTCCATGGATACCCAAAATCTTGGATACCATCTTCCATGGATAGCTTTC
upper sequence: GLYMA19G32190.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g03640.t01 (Vitis vinifera), 3'ss of exon 1
gtagttaattatataacatacgctttttaaaattatttttttatttgattcatgtcttcaagacattttttttaattgaatccttatgtttatatatatagtacttacttttgaagggttttctttgtgcagGTTATTTTAATCTCATTTTCAACTTGGCTTGCATGGTTTTTAGCTGGAAGATTTCATGCTTACCCCAAGTCTTGGATACCATCTTCCATGGATAGCTTTC
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----gtgaacatctaa---atgccttctagtctcctttgtttactttatgcattctaaatagagagatgatttggtttcaggcctttgctaaca-----actgcctatcttt---------------tgcagGTTATTATCCTTTCATTTTCCACTTGGCTTTCCTGGTTTTTAGCAGGAAAGTTTCATAGGTATCCAAAATCTTGGATACCTTCTTCCATGGATAGCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatccttatgtttatatatatagtacttacttttgaagggttttctttgtgcagGTTATTTTAATCTCATTTTCAACTTGGCTTGCATGGTTTTTAGCTGGAAGATTTCATGCTTACCCCAAGTCTTGGATACCATCTTCCATGGATAGCTTTC
tacttac putative branch site (score: 1)
ttttctttgt putative PPT
ttatgtttatatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagttaattatataacatacgctttttaaaattatttttttatttgattcatgtcttcaagacattttttttaattgaatccttatgtttatatatatagtacttacttttgaagggttttctttgtgcagGTTATTTTAATCTCATTTTCAACTTGGCTTGCATGGTTTTTAGCTGGAAGATTTCATGCTTACCCCAAGTCTTGGATACCATCTTCCATGGATAGCTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA