Sequence
atgc intronic sequence ATGC exonic sequence...tttagtgtccatcaattatgctgtttgccaaaaaaatgcaacctttgacagtgttattattcattattttaattccctcatcagtgttctttcccctcagAATCAAAAAAATTTAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
Basic information
species | Glycine max |
transcript | GLYMA04G31180.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g49570.1 (Oryza sativa), 3'ss of exon 7
---tttagtgtccatcaattatgctgtttgccaaaaaaatgcaacctttgacagtgt-tattattcattattttaattccctcatcagtgttctttcccctcagAATCAAAAAAATTTAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
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ttatttagcatgtgtatatagtgcaaatttctgttagttcacc-catttaacagtgaattctacttgctatttgtaa---cgaagagttccttatccttgccagAGTCAGAAAAGTATAAAGCTGTTATCCTCCGTATAGACAGCCCTGGTGGTGATGCTCTTGCTTCTGATCT
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G122843_T02 (Zea mays), 3'ss of exon 12
tttagtgtccatcaattatgct-gtttgccaaaaaaatgcaacctt-tgacagtgttattattcattattttaattccc-tcatcagtgttctttcccct--cagAATCAAAAAAATTTAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
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-----ttcttatagtttatatgagcatatacatattgtgcaaactcatgttatttcaactgacaattccatcacttctaattatgaagcttcttgctatttgcagAATCAGAAAAGTACAAAGCTGTTATCCTACGTATAGACAGCCCTGGTGGTGATGCTCTTGCTTCTGATCT
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G73990.1 (Arabidopsis thaliana), 3'ss of exon 7
tttagtgtccatcaattatgct---gtttgccaaaaaaatgcaacctttgacagtgttattattcattattttaattccctcatcagtgttctttcccctcagAATCAAAAAAATTTAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
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-gtag-gtctgtttattacgttttcatctactagtgtgctgttgtgttcgtcaatagca--gctcagaactttatttcc----------tctttcttttgaagAGTCCAAAAAATATAAGGCTGCCATCATCCGAATTGACAGTCCAGGAGGTGATGCTCTCGCTTCTGATTT
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv17s0000g04690.t01 (Vitis vinifera), 3'ss of exon 3
-tttagtgtccatcaattatgctgtttgccaaaaaaatgcaacctttgacagtgttattattcattattttaattccctcatcagtgttctttcccctc-agAATCAAAAAAATTTAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
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ttcttttgcatatggaaaacaaattttgacttccaatgagtgcttattacatgatt--taggtcttgctttaagctaatgctgggcctttttttctttccagATTCAAAAAGATATAAGGCTGTTATCATTCGCATTGACAGCCCTGGAGGTGATGCTCTTGCTTCTGATTT
upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ14449 (Selaginella moellendorffii), 3'ss of exon 7
tttagtgtccatcaattatgctgtttgccaaaaaaatgcaacctttgacagtgttattattcattattttaattccctcatcagtgttctttcccctcagAATCAAAAAAATTTAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
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----------------------------------------gtctttttct-tgtttagacagacgttttccatttttttcttgac-ttcaacttatgcagAGGCCAAGAACTTTAAAGCCGTTGTTCTCAGAATTGATAGTCCTGGAGGTGATGCACTTGCATCGGACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacagtgttattattcattattttaattccctcatcagtgttctttcccctcagAATCAAAAAAATTTAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
ttttaat putative branch site (score: 3)
tgttctttcccctc putative PPT
tgttattattcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttagtgtccatcaattatgctgtttgccaaaaaaatgcaacctttgacagtgttattattcattattttaattccctcatcagtgttctttcccctcagAATCAAAAAAATTTAAGGCTGCTATCATCAGAATTGACAGTCCTGGAGGTGATGCTCTTGCTTCTGATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - ccatcaa
- - - - - - - - - tgctgtt
- - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - tgcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtgttc