Sequence
atgc intronic sequence ATGC exonic sequence...tcctctttcctaacaatctaacgtagagaaatcagttttatttaacattaatggagagctgagaaaagttgaatttaattcataatcttatggattacagGTTATGGAGAAGCTTGTAGACATTGTCCATTTTTTGCATTTGGAGATAAGCAATGCCTTTGGCAATGCAG
Basic information
species | Glycine max |
transcript | GLYMA06G16680.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------------tcctctttcctaacaatctaacgtagagaaatcagttttatttaacatt---aatggagagctgagaaaagttgaatttaa----ttcataatcttatggatt---acagGTTATGGAGAAGCTTGTAGACATTGTCCATTTTTTGCATTTGGAGATAAGCAATGCCTTTGGCAATGCAG
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gtttgtagtagtttctttgtttataaaatgttggttcaaggaaggcattgggtactacaacgagtacatgtttgaacacaccgaccgcactacgcacatattctattgtcatatcattctttaaatttttagtaaaaaaaaccattctttaaatgctgaaaaatattatgcttttccacagGTGATGGAAAAGCTCGTAGACATTGTTCATTTCTTACATTTGGAGATCAATAATGCCTTTGGCCTCGCTG
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------------------tcctctttcctaacaatctaacgtagagaaatcagttttatttaacattaatggagagc--tgagaaaagttgaatttaattcataatc--ttatggattacagGTTATGGAGAAGCTTGTAGACATTGTCCATTTTTTGCATTTGGAGATAAGCAATGCCTTTGGCAATGCAG
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gttggtcattggttttattatagttcttgctatgagcaacatatagctatatggaagcatgctcacattgtcaattgtgaagttccactcattgattgtccaattgaactagaattcgttttgtgcaatcctgttcgtctaatttgaaaaaaaaacatttatttttcctagGTCATGGAAAAGCTCGTAGACATTGTGCATTTCTTACATTTGGAGATCCATAATGCCTTTGGGCGCTCAG
upper sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0031g02970.t01 (Vitis vinifera), 3'ss of exon 6
--tcctctttcctaacaatctaacgtagagaaatcagttttatttaacattaatggagagctgagaaaagttgaatttaattcataatcttatggattacagGTTATGGAGAAGCTTGTAGACATTGTCCATTTTTTGCATTTGGAGATAAGCAATGCCTTTGGCAATGCAG
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ctgaatacaatctggaaagtcatcattagaaaattg--tgaattagtaaataattagaatttgaaatctcttggagggagatctaacatgagcagactgcagGTGATGGAGAAGCTTGTAGATATTGTCCACTTTTTACATCTGGAGATACGCAATACCTTTGGCACTGTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattaatggagagctgagaaaagttgaatttaattcataatcttatggattacagGTTATGGAGAAGCTTGTAGACATTGTCCATTTTTTGCATTTGGAGATAAGCAATGCCTTTGGCAATGCAG
atttaat putative branch site (score: 4)
aaaagttgaatttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcctctttcctaacaatctaacgtagagaaatcagttttatttaacattaatggagagctgagaaaagttgaatttaattcataatcttatggattacagGTTATGGAGAAGCTTGTAGACATTGTCCATTTTTTGCATTTGGAGATAAGCAATGCCTTTGGCAATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - cctaaca
- - - - - - - - - - - - - - - - - - - - - - - - - -tggagag