Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagattgtgtctatactgaagcatagatatctattggccattgttgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 21
gtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagattgtgtctatactgaa-gcatagatatctattggccattgttgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA
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--------------------------------------gtaagagaaaacactatcggaagtccaaacagttcaatatccgtgaagatcctttagttatttacaataaataatagtttacttgcccttaat---caggtgatgttaagtaactgttgtaatt-tatgcct--ttctcttttatagCTATACAAAATAATGAAAGAGCACAAAAATCCAAAGGTGCTTAGCGAGGGTATTCTTTGGATGGTTTCTGCCGTTGAGGACTTTGGGATCTCCAATTTAA
upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 21
gtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagattgtgtctatactgaagcatagatatctattggccattgttgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA
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--------------------------------------------------------------------------------cactgtcgaacatctttcaattttattctgtgctttaggtgcacgctgcttccaccatgatgtttgacaactactatattt--atgagtttta--tttttatagCTTTACAAAATAATGAAGGAGCACAAGAATCCCAAGGTTCTTAGTGAGGGTATTCTTTGGATGGTCTCTGCTGTGGAAGACTTTGGGATCTCCAATTTAA
upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 3
-------------gtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagatt--gtgtctatactgaagcatagatat-ctattggccattgttgtttcagta-atcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA
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gtaagagataccattagattattattgtttttgttcaaaaggtcctccacatttgttcaatc-aacccaattaggtgattttatatgctggtccgcaataaattcagaatgtgcactgtcgaacatctttgcaattttattttgtgctttagatgcacactgcttatatgatgtataattatgagttttaatttt--gtagCTTTACAAAATAATGAAGGAGCACAAGAATCCCAAGGTTCTTAGTGATGGTATTCTTTGGATGGTCTCTGCTGTGGAAGACTTTGGGATCTCCAATTTAA
upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 23
gtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagattgtgtctatactgaagcatagatatctattggccattgttgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA
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---------------------------------------------------------------------------tataaa-atgcaggttgtatct---tttggccgtatat-catattatttttgtttatctttatgtatt--atcaaataatgtttgaaaaccgtgaat--tttactgtagCTTTACAAGATCATGAAGGAGCATAAGAATCCCAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA
upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 21
gtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagattgtgtctatactgaagcatagatatctattggccattgttgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA
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-----------------------------------------------------------------------ttcatataaa-attcaggttgtaccttt-tggctgtata-atattt-ttgtttatctttat----gtattatcaa----ataatgtttgaaaaactctaa-attttactgtagCTTTACAAGATCTTGAAGGAGCATAAGAATCCTAAGGTTCTTAGTGAGGGAATTTTGTGGATGGTTTCTGCTGTTGAAGATTTTGGTGTCTCACATATAA
upper sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 3'ss of exon 21
gtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagattgtgtctatactgaagcatagatatctattggccattgttgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA
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-----------------------------------------------------------------------------------------------------gtatgtgctggt-tcggtcaactttctttgactt--tcattttattctgatcataatgacatatggct----tttgtttgtagCTTTTCAAAATCATGAAAGAGCACAAGAATCCCAAGGTTCTTAGTGAAGGCTTGTTATGGATGGTTTCGGCAGTTGATGACTTTGGTGTCTCACTTTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA
tcttgac putative branch site (score: 3)
tgctttttt putative PPT
tcatatttttctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcaagtttctatcgggcttgaagcttctgtttctctatttggtttgatataaaaacttccttagaattaatatttttatatagattgtgtctatactgaagcatagatatctattggccattgttgtttcagtaatcttgacttggtcatatttttctatggatgatgcttttttatagCTTTACAAAATCATGAAAGAGCACAAGAATCCAAAGGTCCTTAGTGAGGGCATCTTGTGGATGGTTTCAGCAGTTGAAGACTTTGGTGTTTCACATTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA