Sequence
atgc intronic sequence ATGC exonic sequence...tgcatatgctttgaggaagaaattttttttaattttccatgaacattaattcatgtgcgtttgattaattagttatattgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT
Basic information
species | Glycine max |
transcript | GLYMA17G36300.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G36300.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G142507_T02 (Zea mays), 3'ss of exon 3
tgcatatgctttgaggaagaaattttttttaattttccatgaacattaattcatgtgcgtttgattaattagttatattgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT
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----------gtaatgaagatatatactgggtcatgtgattttcctttttctatttatttccaggttagtgtctgacttgcatgttctttgtctgt-tagGAAAGAATGTGCGTGCACAGGGGTTAGGTTCTTTGCTATCTTGTCAATGCAGAGGTCCGGGAGTGGATGGGTTGAGACGTTGTTGAATAGCCATCCTAAT
upper sequence: GLYMA17G36300.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G877077_T01 (Zea mays), 3'ss of exon 2
tgcatatgctttgaggaagaaattttttttaattttccatgaacattaattcatgtgcgtttgattaattagttatattgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT-----
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----------gtaacgaagatatactgtgtcctctgattttgccttt--ttcaggttagt--gactgacttgt------gggtgttctttgtctgt-taggaaagAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAATATTAG
upper sequence: GLYMA17G36300.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G877077_T02 (Zea mays), 3'ss of exon 2
tgcatatgctttgaggaagaaattttttttaattttccatgaacattaattcatgtgcgtttgattaattagttatattgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT
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----------gtaacgaagatatactgtgtcctctgattttgccttt--ttcaggttagt--gactgacttgt------gggtgttctttgtctgt-tagGAAAGAATGTGCGTGCACGGGGGTTAGGTTCTTTGCTATATTGTCAATGCAGAGGTCAGGGAGTGGATGGGTTGAGACATTGTTGAATAGCCATCCTAAT
upper sequence: GLYMA17G36300.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g11050.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------tgcatatgctttgaggaagaaattttttttaattttccatgaacattaattcatgtgcgtttgattaattagttatattgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT
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gtagctggaaatttgttctctgtttgtgaatgattttgtgtttttttttttttttgggtggggggggggggggggtggggtgggggagtatgggagttcaggc-catttgggt--tcactgaaactgatggtttgttgcatttccagGGAGGAATGTGTGTGTAATGGGGTCCGCTATTTTGCCATCTTGTCTATGCAAAGATCCGGGAGTGGATGGTTTGAGACATTGTTAAATAGTCATATTAAT
upper sequence: GLYMA17G36300.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S310_50V6.2 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------tgcata-tgctttgaggaagaaattttttttaattttccatgaacattaattcatgtgc-gtttgattaattagttat--attgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT
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gttagtttcgtaaacgttgctgcccaagtggttcactatgctcataaattccctataacactttctaaatcagcacttcctt--cttctcatgaaggtcactcctttcgttgtgctatgaaaggcctcttgatttcctgttcgttttgcatgcagGCAAGAGTGCACTTGCACTCCTGTGCACTATTTTGTAATATTATCAATGCAAAGATCAGGAAGTGGATGGTTTGAGACTCTACTCAATAATCACCCAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaattcatgtgcgtttgattaattagttatattgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT
gattaat putative branch site (score: 3)
tttgattaattagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcatatgctttgaggaagaaattttttttaattttccatgaacattaattcatgtgcgtttgattaattagttatattgaatgattggtgaatgagcagAGAGGAGTGTGCTTGCAATCCTGTACGGTTTTTTGTCATATTGACAATGCAAAGATCGGGGAGTGGATGGTTTGAGACGTTGTTGAACAGTCATATGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
tgcatat
- - - - - - - ggaagaaa
- - - - - - - - - - - - - - - - - - -catgaac
- - - - - - - - - - - - - - - - - - - - - - - - - -catgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatga