Sequence
atgc intronic sequence ATGC exonic sequencegtaacttcattttctgatcttgttatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01460.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g03760.3 (Oryza sativa), 3'ss of exon 7
gtaacttcattttctgatcttgttatgctactctataccttgttccttttgtgtctgacc--tggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
| | | || || ||| |||||| ||| | || | | || | || | |||||| | ||||||| ||||| || ||||||||||| |||||||||||||||||||| | || || |||||||||| ||||||||| |||||||| | || ||||| ||
-------------------gtatatttctgttcattacattgttctgaactcgtcctattgatgacagtagcttgaccaatattctgttttctg---tattagGTCTGCTTGGGACTGCTGCCTTTGCATTCTTCTGTTTCTATCTCCTCATAGCAGTGATTGCTGGGGAAATGATGCTGGGTTTGAAATTAGTTTTCATCAC
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 9
gtaacttcattttctgatcttgttatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacatttt--cttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
|| |||||| || | | || | | | ||| || |||| | || || | | || | |||| || |||||| ||||| || ||||| || || |||||||| ||||||||||| |||| || |||||||||| ||||||||||||||||| || || ||||| ||
------gtatcttctga----attctcatcttccagtcttgtcaacttatggtgctgatgagaaca-------atccaattaatcttctaatttgtgtaccagGTCTCCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTCCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGTTTGAAACTTGTTTTCATCAC
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 7
gtaacttcattttctgatcttgttatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacatttt--cttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
| || || | || || | | ||| || |||| | | || || | | || | || | || |||||| ||||| || ||||| || || |||||||| |||||||| || |||| || |||||||||| ||||||||||| |||||||| || || || ||
-----------------gtatcttctgatcttccattcttgtcaacttatgctgctgagccga------acaaattcaattaatcttctgatttatgtaccagGTCTGCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTTCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGATTGAAGCTAGTTTTTATCAC
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 9
-------------------gtaacttcattttctgatcttgt-tatgctactctataccttgttccttttgtg-tctgacctggctctgtgttcat-acatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
|| || ||| || || | ||| || | |||| || | | ||| | | | | | | || | || || |||| | |||| ||||||||||||||| ||||| ||||| || ||||| ||||| || || |||||||| |||||||| || ||||||||||| ||| || || ||||||||
gtatgttggaaaactcaggctatttttctttccttcagttatgtataataattgatacattatattatatgtaatattctttcaattaatctagatgatatatgtaatttgttctttcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTTTTCATTAC
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 8
-------------------gtaacttcattttctgatcttgt-tatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
|| || ||| || || | ||| || | |||| || | | | | | | ||| | | ||| |||| | | ||||| ||| ||||||||||||||| ||||| ||||| || ||||| ||||| || || |||||||| |||||||| || ||||||||||| ||| || || ||||||||
gtatgttggaaagctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatcta-gatgatatatgtaatttgttctt--tcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTTTTCATTAC
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 9
-------------------gtaacttcattttctgatcttgt-tatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
|| || ||| || || | ||| || | |||| || | | | | | | ||| | | ||| ||| | | ||||| ||| ||||||||||||||| ||||| ||||| || ||||| ||||| || || |||||||| |||||||| || ||||||||||| ||| || || ||||||||
gtatgttggaaggctcaggctatttttctttccttcagttatgtataataattgatacattatatgtaatattcattcagttaatcta-gatgatatatgcaatttgttctt--tcatcagGTCTTCTTGGCACTGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGTGCCATGATGCTTGGACTGAGACTAGTATTCATTAC
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 9
----------------------------gtaacttcattttc-tgatcttgttatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
| | | |||| | | | || | | ||| | || || | |||| | | | | | | | ||||| |||| | | |||| ||||||||| || |||||||| ||||| || ||||| ||||| || || |||||||| |||||||| || ||||||||||| ||| || || ||||||||
gtatgttggattactcttacctttagtgattattccattaccataagctagagagtatac---agacattatatattttaattttcattcagttat-tcttcatgatgtctgcattctact-ttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 9
----------gtaacttcattttctgatcttgttatgctact-----ctataccttgtt----ccttttgtgtctgacctg-gctctgtgttcatacatgtgacat---tttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
|| | | || | || || ||| ||||| | | | || | | | | | | || || | | |||| || || | |||| ||||||||| || |||||||| ||||| || ||||| ||||| || || |||||||| ||||| || || ||||||||||| ||| || || ||||||||
gtatgttggaatactcttacctttagtgattattccattaccataagctatagagtatagagacattatatattttattttcattcagtaattcttcatgatgtatgcattcttctttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCCGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC
upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 9
gtaacttcattttctgatcttgttatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
| | | ||| | | || ||| | | | || | ||| || |||| | |||| | | | ||| ||| |||||| | || || || || ||||| |||||||| ||||| || || ||||| || ||||| ||||||||||||||||| | | | || ||||||||
---gtactgctatagatttttgctgt-ctctgttattttatttcctttcactagatgatcttattctg-------agatgtatcttgtacttcttcgtcagGTCTCTTGGGTACTGCAGCATTTGCATTCTTCTGCTTCTACCTTCTGCTTGCGGTGATTGCAGGGGCAATGATGCTTGGACTTAGATTAGTTTTCATTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtgtctgacctggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
gtctgac putative branch site (score: 3)
ttttcttgttcact putative PPT
attttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttcattttctgatcttgttatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG