Sequence
atgc intronic sequence ATGC exonic sequencegtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatccttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttggcccagctttggtgtatttttgttactcagttaaagatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22770.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 6
gtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatccttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggc--ttggcccagc--tttggtgtatttttgttactcagttaaagatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG
|| | | | ||||| | || || || || | | | | ||| || | | | | | | |||| || | | | |||||||||| |||||||||||||||| || ||||| || ||||||||||| | | ||| |||| | ||||||
--------------------------------------------------------------------------------------------------ctggtttgttcaaagaaatatatgcgtctgttgtggccattggatttgtattttctatatgtctccaactgtttttcaagcttaaattttctatat----acagGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 6
gtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatccttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttggcccagctttgg-tgtatttttgttactcagttaaagatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG
|||||| | ||| || | | || || | |||| | | || || |||| || | ||| | |||| ||| ||| | ||| || |||||||||| ||||||| |||||||| || ||||| |||||||||||||||| | ||| ||| ||||||||
--------------------------------------------------------------------------------attttacatctttgattttatgttggcgtgtgaagg--aaaccatgtatatgcattggatggaaccatgt-attcagctaagaata----------------aaatttaattttcacagGTTAAGACAATGAGAGCTCTTCAGTACTTCCCTACCATTGAAGATCCCAACGCAAGACGGGCTTTGTTTGAG
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 7
gtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatccttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttggcccagctttggtgtatttttgttactcagttaaagatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG
|| ||||| | | ||||| | | | | | |||| ||| ||| ||| | | || || | ||| |||||||||| ||||||| |||||||| || ||||| |||||||||||||||| | ||| |||| ||||||||
--------------------------------------------------------------------------------------ttggttctatgttggtgtgttgaaggaaaacatacatgcacattggatggaaatggtccatgtt-ttcaactaagaataacattt-tattttcacatc----------acagGTTAAGACAATGAGAGCTCTTCAGTACTTCCCTACCATTGAAGATCCCAACGCAAGACGAGCTTTGTTTGAG
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 6
gtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatcc--ttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttggcccagctttggtgtatttttgttactcagttaaagatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG
| || | | | || ||| | | | ||||| | || | | |||| || | || || || | | || ||| || ||| | || ||| | | ||| | | || | |||||| | | | | ||| || |||| ||| | |||| || |||||||||||||||||||||| || |||||||||||||| | | | |||| | ||||||||
---------------gtttgtgaatttttctttt-catcaaatatatttctgtattggcttgggttttaggaagatttttgaatgctactcttacagcttgctttta--ttgagaaccaaaagtgttgaactaaattt----tttcttatccagcaagttaacctttt--ttagtgtttaacaatttttgcttaatgtagGTCAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCAAGAAGGTCATTGTTTGAG
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 6
gtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatccttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttggcccagctttggtgtatttttg-ttactcagttaa--agatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG
|| |||| | ||| || || | | ||||| || ||| | | | |||||| ||| ||| | | | | | ||| || |||| ||| | |||| || |||||||||||||||||||||| || |||||||||||||| | | |||||| | ||||||||
---------------------------------------------------------------gtttgtaaatttaggaatatttttgaatgctac-tcttaccagcttgcttttattgagaaccaaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttactcagttaaagatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG
atacttatatatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatccttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttggcccagctttggtgtatttttgttactcagttaaagatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA