Sequence
atgc intronic sequence ATGC exonic sequencegtaagttttcttcattcatttgtgttaatgataagaaaaggggaaaaattgtatgtaagaaaagggggaaaattatgataatataattatgtataggcattcttataagagaaagttataatttggcatgtagtggatagttatctcaaattggttattctggtttttttgacagatgattccttgtcttccagAGTTTTGGGCAGCATGGAAGAGAGCTGATTACCACAGAACTTGCTTTAAGGATTTTGTCTATCTTAAGTGAAGAAAAAATTCTACCCAGCATGGATCAAG
Basic information
species | Glycine max |
transcript | GLYMA06G02070.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G02070.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g02710.2 (Oryza sativa), 3'ss of exon 3
gtaagttttcttcattcatttgtgttaatgataagaaaaggggaaaaattgtatgtaagaaaagggggaaaattatgataatataattatgtataggcattcttataagagaaagttataatttggcatgtagtggatagttatctcaaattggttattctggtttttttgacagat-gattccttgtcttccagAGTTTTGGGCAGCATGGAAGAGAGCTGATTACCACAGAACTTGCTTTAAGGATTTTGTCTATCTTAAGTGAAGAAAAAATTCTACCCAGCATGGATCAAG
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------------------------------------------------------------------------------------agcaaaacaaaaccaactttttgata-atttttacacattggcttgta------aattaaatta--ttgatg--tcttgcggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAGCTTATCACTTCTGAAGTTGCATTAAACCTCCTCTATATTTTGACCGAGAAGCGGAAAATTGCTGGTGTCGATCTAT
upper sequence: GLYMA06G02070.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G006069_T02 (Zea mays), 3'ss of exon 2
gtaagttttcttcattcatttgtgttaatgataagaaaaggggaaaaattgtatgtaagaaaagggggaaaattatgataatataattatgtataggcattcttataagagaaagttataatttggcatgtagtggatagttatctcaaattggttat-tctggtttttttgacagat-gattccttgtcttccagAGTTTTGGGCAGCATGGAAGAGAGCTGATTACCACAGAACTTGCTTTAAGGATTTTGTCTATCTTAAGTGAAGAAAAAATTCTACCCAGCATGGATCAAG
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----------------------------------------------------------------------------------aagataataaacatgtattttcattagt----------atttg---tgtgttgattagtaaatt-aaattattgataccttgtggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGTCTTCTCTATGTTTTAACGGAGAAGCCCAAGATCGCTGGTGTGGATATTT
upper sequence: GLYMA06G02070.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G42320.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttttcttcattcatttgtgttaatgataagaaaaggggaaaaattgtatgtaagaaaagggggaaaattatgataatataattatgtataggcattcttataagagaaagttataatttggcatgtagtggatagttatctcaaattggttattctggtttttttgacagatgattccttgtcttccagAGTTTTGGGCAGCATGGAAGAGAGCTGATTACCACAGAACTTGCTTTAAGGATTTTGTCTATCTTAAGTGAAGAAAAAATTCTACCCAGCATGGATCAAG
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gtaagttcccttca--cagctctgtctaagctattcacagg---aatatcaaataaattgacaaatcccgtcttctggt---ttaact-tgta-atacttttttataggtgaagtttcttc---------------atagtt--------ttggtaatacctgtttttttgacagatgattccttttcttccagACTTTTGGTCAGCATGGGAGAGAGCTTATCACCTCTGAACTTGCTTTTCGGATTTTGTCAATTTTGAGCGAAGAACAGTTCTTACCAAATAAAAACGGAG
upper sequence: GLYMA06G02070.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0122g01410.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttttcttcattcatttgtgttaatgataagaaaaggggaaaaattgtatgtaagaaaagggggaaaattatgataatataattatgtataggcattcttataagagaaagttataatttggcatgtagtggatagt-tatctcaaattggttatt-ctggtttttttgacagatgattccttgtcttccagAGTTTTGGGCAGCATGGAAGAGAGCTGATTACCACAGAACTTGCTTTAAGGATTTTGTCTATCTTAAGTGAAGAAAAAATTCTACCCAGCATGGATCAAG
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-----------------------------------------------------------------------------------------------agtact-ttgcaggccttatcttcaaatttacatgtagtggatagaatatctcagattggtatttgctggtttttttgacagatgattccttgtcttccagAGTTTTGGGCAGCATGGGAGGGAGCTCATTACATCTGAACTTGCATTGCGGGTCCTATCAGTGTTGAGTGAAGAACAGTTTCTACCCAACATGGATCCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttatctcaaattggttattctggtttttttgacagatgattccttgtcttccagAGTTTTGGGCAGCATGGAAGAGAGCTGATTACCACAGAACTTGCTTTAAGGATTTTGTCTATCTTAAGTGAAGAAAAAATTCTACCCAGCATGGATCAAG
ttttgac putative branch site (score: 3)
ttccttgtcttcc putative PPT
tttttttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttttcttcattcatttgtgttaatgataagaaaaggggaaaaattgtatgtaagaaaagggggaaaattatgataatataattatgtataggcattcttataagagaaagttataatttggcatgtagtggatagttatctcaaattggttattctggtttttttgacagatgattccttgtcttccagAGTTTTGGGCAGCATGGAAGAGAGCTGATTACCACAGAACTTGCTTTAAGGATTTTGTCTATCTTAAGTGAAGAAAAAATTCTACCCAGCATGGATCAAG
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