Sequence
atgc intronic sequence ATGC exonic sequence...tgttgggtattcatctgtaattctcggtttcatagagttttgtgatgtttttggatcttttttttgtttatgaagtttggatttttttttatttggtcagGTATTTACATAATCAATCTTGGAAAGACATGGGACAAGCTTCAGATGGCTGCTAGGGTTATTGTAGCAATCGAAAACCCAAAAGACATAATTGTTCAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04770.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G159237_T02 (Zea mays), 3'ss of exon 1
---tgttgggtattcatctgtaattctcggtttcatagagttttgtgatgtttttggatct--tttttttgtttatgaagtttggatttttttttatttggtcagGTATTTACATAATCAATCTTGGAAAGACATGGGACAAGCTTCAGATGGCTGCTAGGGTTATTGTAGCAATCGAAAACCCAAAAGACATAATTGTTCAATC
| | | |||| ||| || ||| | || | || | || || | || | || || || | || | | |||| | |||||||| ||||| || || ||||||||||| ||||||||||||||| |||| || ||||| || || || || || || || | ||||| || || || ||
aatggctcgtagttcagtgctaactcg-agttgctta---tgctggcaatttcttatacctaacagtagtgcttttgtatattattatcatcattatctt-tcagGTATCTACATTATTAACCTTGGAAAGACCTGGGACAAGCTTCAGTTGGCCGCCAGGGTCATCGTTGCCATTGAGAATCCGCAGGACATTATCGTGCAGTC
upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G17000.1 (Glycine max), 3'ss of exon 1
----------tgttgggtattcatctgtaattctcggtttcatagagttttgtgatgtttttggatcttttttttgtttatgaagtttggatttttttttatttggtcagGTATTTACATAATCAATCTTGGAAAGACATGGGACAAGCTTCAGATGGCTGCTAGGGTTATTGTAGCAATCGAAAACCCAAAAGACATAATTGTTCAATC
||| | | || | ||| | | || | | || |||| | | ||| || ||| || |||| ||||||| |||||||||||||||| || ||||||||||||||||| ||||||||| | ||||||||| |||| || || || || |||||| | || || || ||||| ||
tttttttttttgtaccgctgttatgaagatttcctcttgctactgaaata-gagacattttggagtttttgttgaatttttgtggtttatgttttttt---------cagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTGCTAGGATTATAGTCGCCATTGAGAACCCACAGGATATCATCGTTCAGTC
upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G42150.1 (Glycine max), 3'ss of exon 1
tgttgggtattcatctgtaattctcggtttcat-agagttttgtgatgtttttg-----gatcttttttttgtttatgaagtttggatttttt---tttatttggtcagGTATTTACATAATCAATCTTGGAAAGACATGGGACAAGCTTCAGATGGCTGCTAGGGTTATTGTAGCAATCGAAAACCCAAAAGACATAATTGTTCAATC
|| || | | || | ||| | |||| | || | || || | |||| |||| || ||| |||||| ||||| | ||||||||||||||||| || ||||| ||||||||||| ||||| ||| | ||||||||| ||||||| || || || |||||| | || || |||||||| ||
-----ggcgtttgcttttttgcaccgctaccatgaaggtttcctcttgctactgaaatagaacattttggagtttttg----ttgaatttttgtggtttatgttttcagGTATTTACATAATTAACCTTGGCAAGACATGGGAGAAGCTCCAGCTCGCTGCTAGGATTATTGTTGCCATTGAGAACCCACAGGATATCATTGTTCAGTC
upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G01460.1 (Glycine max), 3'ss of exon 1
-------------------------tgttgggtattcatctgtaattctcggtttcatagagt-------tttgtgatgtttttg---gatcttttttttgtttatgaagtttggatttttttttatttgg---tcagGTATTTACATAATCAATCTTGGAAAGACATGGGACAAGCTTCAGATGGCTGCTAGGGTTATTGTAGCAATCGAAAACCCAAAAGACATAATTGTTCAATC
| || || | || | ||||| | | | || || | | || || | || || ||||| | ||| |||||| | ||| |||||||| || || ||||| ||||||||||| ||||||||| | || |||||||||||||| ||||| || ||||| | || || |||||||||||
gtaactgaacttttctcgttctctcttttatcatctcgttaaaaaaattaaatttcaatggatgtttgaatctgcaatagctgtaatagaggaattgaattttgatttgatttggtgtggtttggatttgggaattagGGATTTACATTATTAACCTTGGGAAGACATGGGAGAAGCTTCAGTTAGCAGCTAGGGTTATTGTTGCAATTGAGAACCCTCAGGATATCATTGTTCAATC
upper sequence: AT3G04770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G04890.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------tgttgggta-ttcatctgtaattctcggtttcatagagttttgtgatgttttt-------ggatcttttttttgtttatgaagtttggatttttttttatttggtcagGTATTTACATAATCAATCTTGGAAAGACATGGGACAAGCTTCAGATGGCTGCTAGGGTTATTGTAGCAATCGAAAACCCAAAAGACATAATTGTTCAATC
|||| | || | | | | |||| | || | | || || | |||| | |||||| || ||| | | || | | ||| |||||||| || || ||||| ||||| ||||| ||||||||| | || ||||||||||| || ||||| || ||||| | || || |||||||||||
gtaactaaaaccctagctcatcctctcttttcatcgatctctgacaatcgcatgttaaacaatttaaattccaatggatgtttgtttgaacct-gcaatagttgtaatagacggatttgatttttgatttgctgtgttgtgctgtggattttggaattagGGATTTACATTATTAACCTTGGGAAGACGTGGGAGAAGCTTCAGCTAGCAGCTAGGGTTATAGTTGCAATTGAGAACCCCCAGGATATCATTGTTCAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttttggatcttttttttgtttatgaagtttggatttttttttatttggtcagGTATTTACATAATCAATCTTGGAAAGACATGGGACAAGCTTCAGATGGCTGCTAGGGTTATTGTAGCAATCGAAAACCCAAAAGACATAATTGTTCAATC
tttttttttattt CT-rich tract
ttttttttgtttatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgttgggtattcatctgtaattctcggtttcatagagttttgtgatgtttttggatcttttttttgtttatgaagtttggatttttttttatttggtcagGTATTTACATAATCAATCTTGGAAAGACATGGGACAAGCTTCAGATGGCTGCTAGGGTTATTGTAGCAATCGAAAACCCAAAAGACATAATTGTTCAATC
- - - - - - - - - - - - - - - - - - gttttgt
- - - - - - - - - - - - - - - - - - - - - - - gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtttgg