Sequence
atgc intronic sequence ATGC exonic sequence...ttgttttcttggtatatttttttattccatcaacgattcacaatttttatgcttcctgctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
Basic information
species | Glycine max |
transcript | GLYMA05G31200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 1
-ttgttttcttggtatatttttttattccatcaacgattcacaatttttatgcttcctgctgctagactgctgacaaaattttttgt-tatgtaaat--ttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
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gtggaatttcccgcatgcatgtca--tatatta-tgcttgacagaatgta-gtatgttagtaatttgcttcttacgccttttgtcacatgtgtacttggtccagGCAACGATTGGCATTGACTTTCTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTG
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------------------ttgttttcttggtatatttttttattccatcaacgattcacaattttta----tgcttcctgctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
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gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcag-aattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatggt-gtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
-ttgttttcttggtatatttttttattccatcaacgattcacaatttttatgcttcctg--ctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
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tagatcatgtagatacaatgctgaatgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtt---tcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
--------ttgttttcttggtatatttttttattccatcaac--gattcacaatttttatgcttcctgctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
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aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaa-----ttagttacattctcttgatactcctttttggta-----attgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
upper sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 2
---------ttgttttcttggtatatttttttattccatcaacgattcacaatttttatgcttcctgctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
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tgttcatgtgcgaaaatctgatgcacgaaaatattgt-tcaatttttcaaaacttcgaagtgttctgtggttatggtgataaccaaattttatgtt--------tgcagGCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatgcttcctgctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
tgctgac putative branch site (score: 2)
tgacaaaattttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttttcttggtatatttttttattccatcaacgattcacaatttttatgcttcctgctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - ccatcaa
- - - - - - - - - - - - - - - - - -attcaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttatg