Sequence
atgc intronic sequence ATGC exonic sequence...ctcttacaattattgtgatatttcgtgatgaaatgtttccattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53520.4 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 1
ctcttacaattattgtgatatttcgtgatgaaatgttt-ccattgggaatgtgtttttctctattgttgatatgatg---attctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG------
|| | || | | | | ||| || || | ||| ||| | | | | | | ||| | | ||||| | | |||||| || | ||||||||| ||||| ||||| || | |||||||||||||| |||||| || |||| |||||||| |||| || |||||||||||||| |||||||
------catgtttttttgcaacttattatgttattttcactatttacaatataatcatgtgttgcatctgtatattatcaaatctgggt--ttcttaacaat--tattacAAGACCAATGTCATGGGAACCTTGAATATGTTGGGTCTGGCAAAGCGAATTGGTGCAAGGTTCTTGCTAACTAGCACAAGTGAAGTTTATGGAGATCCAC
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G370048_T01 (Zea mays), 3'ss of exon 2
ctcttacaattattgtgatatttcgtgatgaaatgtttcc-attgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG------
| | | || | ||| || | || | | | || | || | | | | | ||| | |||||| | || |||||||||||||| ||||| ||| | |||||||||||||| |||||| ||||||| ||||||||| || | || |||||||||||||| ||||| |
---atcaatcccctccaatccgtatggattgaaaataaccgaacaagccctaaatgttttgagtttcttttgtctaaaatttggac--ttcttaacact--ttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCAAAGCGAGTTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCAC
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G359234_T03 (Zea mays), 3'ss of exon 1
ctcttacaattattgtgatatttcgtgatgaaatgtttccattgggaatgtgttt---ttctctattgttgatatgatgattctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG---------
| | | | || ||| | |||| |||||| | || | | | | | || | | | || | ||| | |||||| | || |||||||||||||| ||||| ||| | |||||||||||||| || ||| || |||| ||||||||| || | || |||||||||||||| ||||| |
-----aaggatgtcgccattttttgcagc---atgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggac--ttcttaacact--ttgtacaagACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGCTTG
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
ctcttacaattattgtgatatttcgtgatgaaatgtttccattgggaatgtgttt---ttctctattgttgatatgatgattctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG------
|| || | |||| || |||| |||||| | || | | | | | || | | | || | ||| | |||||| | || |||||||||||||| ||||| ||| | |||||||||||||| || ||| || |||| ||||||||| || | || |||||||||||||| ||||| |
----gggaaggatgtcgccattttttg-cagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggac--ttcttaacact--ttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G05260.1 (Glycine max), 3'ss of exon 1
------ctcttacaattattgtgatatttcgtgatgaaatgtttccattgggaatgtgtttttctcta-ttgttgatatgatgattctggtt----gatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG------
|| | | || | | | | | ||| || | | ||||| || || || || | || | || ||||||||| | | ||||||||| ||||| |||||||| || || ||| | || ||||| |||||| ||||||| ||||||||||| || || || ||||| || || || |
atatccttcctctctatgttctaactctgactcgccgtgtttttaagttccagctctcttttttcgtaattttttatgttttgtgttgaattctgtgatccttaattgttggcttacAAGACGAATGTGATGGGCACGCTTAACATGCTTGGCCTTGCGAAGAGAATTGGGGCTAGGTTTCTGCTTACTAGTACTAGTGAGGTTTACGGTGATCCGT
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 1
--ctcttacaattattgtgatatttcgtgatgaaatgtttccattggg----aatgtgtttttctctattgttgatatgatgattctggt----tgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG------
|| | | ||| || || | | | |||| || | ||| | ||| | | || ||| || | || |||||||||| || |||||||||| ||||| |||||||| || || ||| | || ||||| ||| || ||||||| ||||||||||| || || || ||||| || || || |
atatccttgtctcgatgttctaactc-taactcagcgttttttttaagttctaataactcttttttcgtaatttttattttgcgttgagttctgtgatccttaattattagtttacAAGACGAATGTGATGGGCACGCTTAACATGCTTGGCCTTGCGAAGCGAATTGGGGCTAGGTTTCTGCTTACTAGTACTAGTGAGGTTTACGGTGATCCGC
upper sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
ctcttacaattattgtgatatttcgtgatgaaatgtttccattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG---------
| || | | || | || | ||||| || ||| | | || ||| || |||||| || | | |||||||||||||| |||||||| || || |||||||| ||||||||||| |||||||||||||| ||||||| || ||||||||||| ||||| |
------agggtgcca-aatgatgaataatttaggattcaaaaaccaaatgtaaggttagtgattttgtgaaatttggatctcttttatccttgactgtgat--tacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG
ccttaac putative branch site (score: 3)
tcctt CT-rich tract
tgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcttacaattattgtgatatttcgtgatgaaatgtttccattgggaatgtgtttttctctattgttgatatgatgattctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG
- cttacaa
- - - - - - - - - - - - - gatgaaa