Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgcaattctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
Basic information
species | Glycine max |
transcript | GLYMA14G04010.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G04010.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
gtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgcaattctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
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-----------------------------------------------gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttgaaattttaactaacaatgcaatttttggttgttaatt-----------agATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
upper sequence: GLYMA14G04010.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g41270.1 (Oryza sativa), 3'ss of exon 3
gtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgcaattctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
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---------------------------------------------gtgagtacccttcactttacgctgaacat--------cccaaatctttcaacaccctgaatttttcaggtgaatgatgctgtttttgttttctgtc-----cagATCATCCATGGATAAAGGAAGACGGCGAGGCGCCCGATACGCCGCTCGACAATGCTGTTCTTGGCAGGCTCAAGCAGTTCAGAGCTATGAACCAGTTCAA
upper sequence: GLYMA14G04010.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgcaattctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
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------------------------------------------------------------------------gtaagcatctacaaaatatataaaaactgtaaaagcataacaatatattatctctaatgttatcttcctttgtaaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
upper sequence: GLYMA14G04010.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G19360.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgca-attctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
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--------------------------------------------------------------gtaagcagctcttatctta--------aaa--gctcctatatatatttcattgaactcttcttgacatttttgttgttttaa----agATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
upper sequence: GLYMA14G04010.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g03150.t01 (Vitis vinifera), 3'ss of exon 3
gtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgcaattctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
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----------------------------actgagtttggagatatttaggaaaactttgtttgaagtcatacttaattatgatgttagcca-----ttgcacatttttctgataaaat-----tcaattttttctt-----------agATCATCCATGGATTAAGGAGGATGGAGAAGCACCTGATACTCCTCTTGACAATGCAGTTTTTGAAAGGTTCAAACAGTTTAGAGCAATGAACAAGTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttcaatgcaattctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
ttctaat putative branch site (score: 2)
tcttttttattttttt putative PPT
aatgcaattctaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtataatattgacttcctttctatgaacatcttgaattcaactaggaattcttgatttgcaaattaattttactttagcccagacaaattggttcaatgcaattctaataaagtcttttttatttttttattttgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAATGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACCAATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA