Sequence
atgc intronic sequence ATGC exonic sequence...atttttgatattctagtcaacaattatgatattttacatttacctcttgaatctctataaatactagtgtttgacgcaagtgatattgattgtgttgcagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G76270.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os08g44015.1 (Oryza sativa), 3'ss of exon 7
atttttgatattctagtca-acaattatgatattttacatttacctcttgaatctctataaatactagtgtttgacgcaagtgatattgattgtgttgc-agGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
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gattttcttgtatgagtaatataagtatgttgtctatttagtttgtagtggtttccttttttttccttttccctaaacagtctttctc--ttgggttgccagATTTGAACCTGATATGCTTGCATTTTCGGGGTGCTATTATGGTGGTGGAGAAAAAGAAAGAAAAGAGCTTGGTGCAATACGGAAGAGATGGAAAACCTTG
upper sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 10
atttttgatattctagtcaacaattatgatattttacatttacctcttg-aatctctataaat--actagtgtttgacgcaagtgatattgattgtgttg-cagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
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-aagtagagactaaaat-aacatttc--atatgtacactcttcctcttgcactatgcatcattttgctctttttttcagcatgcaccgtctatcctgatggcagGTTTGAACCTGACATGCTTGCCTTTTCTGGGTGTTATTATGGTGGTGGAGAAAAGGAGAAAAGAGAACTAGGCTCCATTCGCAAGCGATGGAAAACTTTG
upper sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G131699_T01 (Zea mays), 3'ss of exon 7
atttttgatattctagtcaacaattatgatattttacatttacctcttgaatctctataaatactagtgtttgacgcaagtgatattgattgtgttg---cagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
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---ttacaaataccttttctcagcgcatatgcgtttcctttacggtaatgatattgattttttcttgtccctttcttaaacattattccttttgcaatgtcagATTCGAACCTGATATGCTTGCCTTTTCGGGGTGCTATTACGGTGGTGGAGAGAAAGAGAGGAGAGAACTTGGTGCTATAAGGAAGAGGTGGAAAGGCTTG
upper sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G168614_T01 (Zea mays), 3'ss of exon 6
-----atttttgatatt-ctagtcaacaattatgatattttacatttacctcttgaatctctataaatactagtgtttgacgcaagtgatattgattgtgttgcagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
|| | | | || || | | | ||| | ||||| | || | ||||| | || | || | | | ||| | | |||| | ||||||||| |||||||| || || || ||||||||||||||||| || ||||| ||||||||| | || |||||| | || |||||| ||| ||
gtgaaatatatcttgttacttctttattactattccgtacaacattagctcgttttgtttctat-----ttcttgaccaagacatg-gttgttgttctgatggcagATTTGAACCTGACATGCTTGCCTTTTCTGGGTGCTATTATGGTGGTGGAGAAAAGGAGAGGAGAGAATTAGCTGCAATTCGCAGACGATGGAGAACCTTG
upper sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G02010.1 (Glycine max), 3'ss of exon 7
-atttttgatattctagtcaacaattatgatatt-ttacatttacctcttgaatctctataaat-actagtgtttgacgcaagtgatattgattgtgttgcagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
| | || || | || | | ||| ||| || | | | || | | || | | | | | || || || | ||| | ||||||||||||||||||||| || ||||| |||||||||| || || ||||| || ||||| | ||||| |||||||| ||||| ||||||
tgtggcttttaccct--tttgcattcaagatgcagttaaataggtagaataacggatgacaagtgaataatttctaaaattgattgcctttttt-tgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGAAGGAGGTGGAAGACATTA
upper sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G02110.1 (Glycine max), 3'ss of exon 6
-atttttgatattctagtcaacaattatgatatt-ttacatttacctcttgaatctctataaat-actagtgtttgacgcaagtgatattgattgtgttgcagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
|| | ||| || | ||| | | ||| ||| || | | | || | | || | | | | | || || || | ||| | ||||||||||||||||||||| || ||||| |||||||||| || || ||||| || ||||| | ||||| || ||||| ||||| ||||||
aatggcttttatact--tttacattcaagatgcagttaaataggtagaataacagatgacaagtgaataatttctaaaattgattgcctttttt-tgctacagATTTGAACCTGATATGCTTGCATTTTCTGGATGTGATTATGGTGGAGGGGAGAAGGAGCAGAAGGAACTGGGTGCAATAAGGAGGAGGTGGAAGACATTA
upper sequence: AT1G76270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g00100.t01 (Vitis vinifera), 3'ss of exon 7
atttttgatattctagtca-acaattatgatattttacat-ttacc--tcttgaatctctataaatactagtgtttgacgcaagtgatattgattgtgttgcagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
|| | | | | | | ||| | ||||| | | | || | ||| | || | | | || | || ||| | || ||||| |||||| ||||||||||||||||| |||||||| |||||||| || || |||||||||| ||| || | ||||| ||| ||| |||||||| |||
atgaacaa-gtcatggctatatgattttaatattcaagaaactgccaattatgagaaggtgagaaagtttctttatgccatcagatgctttgtt---gtcacagGTTTGAACCCGATATGCTTGCATTCTCAGGATGCTACTATGGTGGGGGAGAAAAGGAAAGGAAAGAGCTGGGTGCAATACGAAAGAGGTGGAAAACTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgaatctctataaatactagtgtttgacgcaagtgatattgattgtgttgcagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
tattgat putative branch site (score: 3)
tataaatacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttttgatattctagtcaacaattatgatattttacatttacctcttgaatctctataaatactagtgtttgacgcaagtgatattgattgtgttgcagGTATGAACCTGATATGCTTGCATTCTCGGGATGCTATTATGGTGGTGGTGATAAGGAAAGGAGAGAACTTGCAGCAATTAGAAGGAGATGGAAAACATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - -caacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acgcaag