Sequence
atgc intronic sequence ATGC exonic sequence...gaaatgttctatgaaaccactcatgcatcttcacttcacctatcaacttaagcttttgcaatagttgttcccatgacaaacattgctaatttgttggcagGGAGGCCATCATTCACAAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
Basic information
species | Glycine max |
transcript | GLYMA14G06340.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 7
gaaatgttctatgaaaccactcatgcatcttcacttcacctatcaacttaagcttttgcaatagttgttcccatgacaa----acattgcta--atttgttggcagGGAGGCCATCATTCACAAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
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-----attccaccccattcttctccttgtaggccattaacagtgaataaatgttcatggataaatcattcctctgttcactcgttcttcctatcatttattt-cagGGAAACCAGGGTTTTCCAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTCAGGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 7
gaaatgttctatgaaaccactcatgcatcttcacttcacctatcaacttaagcttttgcaatagttgttcccatgacaa----acattgcta--atttgttggcagGGAGGCCATCATTCACAAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
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-----attccaccccattcttctccttgtaggccattaacagtgaataaatgttcatggataaatcattcctctgttcactcgttcttcctatcatttattt-cagGGAAACCAGGGTTTTCCAAGAAGCAAGCTGATCTCTTCTTCCCCCCAGATTTTCAGGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 7
gaaatgttctatgaaaccactcatgcatcttcacttcacctatcaacttaagcttttgcaatagttgttcccatgac-aaacattgctaatttgttggcagGGAGGCCATCATTCACAAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
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-----gttagcttaaactactgctctatattttcatggt-tattg--ttag---ttggtattagt----ctgatgtttaaaggtgggcggctttttttcagGGAAACCATCATTTACAAAAAAGCAGGCAGATCTCTTTTTCCCCCCAGATTTTGCTGATGATTTTCCTGTGGCCATGCAG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
--gaaatgttctatg--aaaccactcatgcatcttcacttcacctatcaacttaagcttttgcaatagttgttcccatgac----aaacattgctaatttgttggcagGGAGGCCATCATTCACAAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
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gttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgttttctaggttgt-attcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 7
-----gaaatgttctatgaaaccactcatgcatcttcacttcacctatcaacttaagcttttgcaatagttgttcccatgacaaacattgctaatttgttggcagGGAGGCCATCATTCACAAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
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gactcactactcttggtggaatcattatgttaccttttattttgttttgaatt----ctgttcttatgtttattcctgtt-ctaacttcaataatttcttagcagGGAAACCAGGATTTACAAAGAAACAGGCTGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCAATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttaagcttttgcaatagttgttcccatgacaaacattgctaatttgttggcagGGAGGCCATCATTCACAAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
tgctaat putative branch site (score: 2)
taatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaatgttctatgaaaccactcatgcatcttcacttcacctatcaacttaagcttttgcaatagttgttcccatgacaaacattgctaatttgttggcagGGAGGCCATCATTCACAAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - -aaaccac
- - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - -cttcacc
- - - - - - - - - - - - - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacat