Sequence
atgc intronic sequence ATGC exonic sequencegttcaccctttttagtcaacagatgtattttctaggtttgcaaccagataaaattaggaggataaactttttgacaaagcaacttgtatgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51820.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 15
gttcaccctttttagtcaacag-atgtattttctaggtttgcaac----cagataaaattaggaggataaactttttgacaaagcaacttg--tatgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
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--gtacttttgtcagtgaattgcatgtgcatgatttgtttgcaaaatagtcaataggccatggcttctagaagaacagctaagacaatatggtcactttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 15
-----------------gttcaccctttttagtca-acagatgtattttctaggt-ttgcaaccagataaaattaggaggataaactttttgacaaagcaacttgtatgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
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gtaccattgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacctgtaatttctacttgatca--tctaagactaagatgcc---acttcttagGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 15
gttcaccctttttagtcaacagatgtattttct--aggtttgcaaccagataaaattaggaggataaactttttgacaaag----caacttgta-------------tgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
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gcatgctttattttttttacaattctttcttcttaaaatattaatataaatgaaataggcttcacatatttttagacatagttctcaaataacaagagatgggccctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 15
gttcaccctttttagtcaacagat--gtattttctaggtttgcaac-cagataaaattaggaggataaactttttgaca------aagcaact-----tgtat----gttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
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gcatgctttatttttcttacaatttctttcttcttaaattattaatataaatgaaataggcttcacatatttttagacagttctgaaataacaaaagatggacccgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCGGTTTGCGGGGAAGAAAGTTTTGGAACAGGTTCTGACCACATTCGTG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
-------------------gttcaccctttttag--tcaacagatgtattttcta---------ggtttgcaacca--gataaaatta------ggaggataaactttttgacaaagcaacttgtatgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
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gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaccagataaaattaggaggataaactttttgacaaagcaacttgtatgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
ttttgac putative branch site (score: 3)
ataaacttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcaccctttttagtcaacagatgtattttctaggtttgcaaccagataaaattaggaggataaactttttgacaaagcaacttgtatgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT