Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctaattactttgtttggcctcaattaatttgggttggttagttaacaattgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G80400.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 2
------------------------gtaagtctaattactttgtttggcctcaattaatttgggttggtta-gttaacaattgttaatgactggc-----agGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
| ||| | || | | || | ||| | ||| | ||| | || | | || | ||| | || | || | ||||||||||||||||| | |||||||||||||| ||||||||||| || || ||||| ||||||||||| || | || |||
ctgaagcatctgtgtatgagcattgcaaggaacactattgt-ttagattgttatttacacatgttcacaatgttgctatttaaagacaaatgccttttcagGATTAATGCTCTTTTTGACCACTTCAAGATGGCCTTGGATTGTTTCTTTGCTGTGTGGTTTGTCGTAGGAAATGTGTGGATATTTGGCGGGCGTTCTTCT
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
----------------------gtaagtctaattactttgtttggcctcaatta-atttgggttggtt----agttaacaat--tgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
| | | | | || ||| || | | | |||||| || || || ||||||| | || | ||| || ||| | || | |||||| |||| | |||||||||||||| |||||||||||||| |||||||| |||||||| || || | | |||
atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatttggattcatttatgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g08610.4 (Oryza sativa), 3'ss of exon 3
----------------------------gtaagtctaat-tactttgtttggcctcaattaatttgggttggttagttaacaattgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
||||| | | ||| || | || | | | | || || | || | ||| || | | | | || |||||||| ||||| | || ||||||||||| |||||||| |||||||| ||||||||| ||||||| || || || |||
aataaactacgtatggtcttccagagatttaagtttcccatgttttattaacttttcctttagtccaagttctgagctacagtcttaccatttgttttagGTTCCAAGCTTTTGCTGATCACTTCAAAATGGCTCTGGACTGTTTCTTTGCTGTGTGGTTCGTTGTGGGAAATGTATGGGTATTTGGTGGACATTCTTCT
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G089466_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------gtaagtctaattac--tttgtttggcctcaat----taatttgggttggttagttaacaattgttaatg---------actggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
|| || | | | |||||| | | | | | ||| || | || | |||| | ||||| |||| | ||| | ||||||||||||||||| | |||||||||||||| || ||||||||||| || || || ||||||||||| || | || |||
gtactcatgccttctttttttccttaaaaaaatggatcggtatttacaatgaatatgtttgactgtcacttgttttgtttatttatggtgctgcaaaatggctatgcattaaagatgaatgccctgtgctatctgcagGATCAATGCGCTGTTTGACCACTTCAAGATGGCCCTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTTGGAAACGTGTGGATATTTGGTGGCCGTTCTTCT
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G004799_T01 (Zea mays), 3'ss of exon 2
-------------------gtaagtctaattactttgtttggcctcaattaatttggg---ttggttagttaacaattgttaatg-actg------gcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
|| | | |||||| | ||||| || || ||| | | || || | | | | | | ||| | ||| | || | | ||| || ||| | | |||||||||||||| || |||||||||||||| ||||| ||||| ||||| | | || |||
ttagtatttgaaatgcatcctataaatggtgcaaatgtttgaagttttttaatatgatattttcgttcataatgaagtgatgacgcattaatctatgtagGTTTTACGCAATGGTTGCCTGCTTTAAATTGGTGTTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTGGGAAATGTGTGGATGTTTGGTAGCCGTTCTTCT
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 2
-------------------------gtaagtctaattac-tttgtttggcctcaattaatttgggttggttagtta---acaattgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
||||||||| | | | | | | | | | || | | | || || | | | ||||||| ||||| |||| ||||| ||||||||||| | ||||| |||||||| || |||||||| || || ||||| ||||| |||||||||||| | |||
ttcaacttaatacaaaaccttgatgcccagtctaattttatccatgtttaatgagtcactagcagcacactaagcagagaaatttcttgctaaattgcagGCTTAACGGATTAGTAGACCATTTCAAGATGGCCTTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G01570.1 (Glycine max), 3'ss of exon 2
-----------------------gtaagtctaatt--actttgtttggcctcaattaatt--tgggttggttagttaacaa--ttgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
| | | ||| | ||| | | ||| ||| | | | || | || || || | | | ||||||| || || |||| ||||| ||||||||||| | ||||| |||||||| || |||||||| || || ||||| ||||| |||||||||||| | |||
caaatcaacttaatacaaaaccttgatgccgaatctaattttatccatgtttaatgaatcactagcacactaagcagagaaatttcttgctaaattgcagGCTTAATGGATTAGTAGACCATTTCAAGATGGCCCTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 3'ss of exon 2
-------------------gtaagtctaattactttgtttggcc--tcaattaatt-tgggttg-gttagttaacaatt--gttaatgactgg----cagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
| | ||| ||| | | || ||||| | || | ||| | ||||| || | | || ||| |||| ||| || | |||||||| || |||||||| | || || |||||||| ||||||||||||||||| ||||| |||||||||||||||||||| |||
tctgatagttaattattttaaacttttaacccttttttgtatccattcaataatttatatattgtatcggttaatgatgtagctgatttctgatacccagGTTCAGTGGAATGGTGGACCATTTTAAGATGGCCTTGGACTGCTTCTTTGCAGTGTGGTTTGTTGTGGGCAATGTGTGGATATTTGGAGGTCACTCTTCT
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ36853 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtctaattactttgtttggcctcaattaatttgggttggttagttaacaattgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT---------
||| | | || |||| || | | | | || | || | | | | | | ||| | |||| ||||| | |||||||| ||| | ||||| ||||| ||||||||||| || || ||||| || ||||||||||| || ||||| ||
gtatgg-tgcttccttttgctgtcttttttatacttttctctattgttcttcgactaatc-tattcatcagtgttggaagGCTGGTGGAGAAGTTCAAGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCGTCCCGCGAA
upper sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ27808 (Selaginella moellendorffii), 3'ss of exon 1
-------------------------------------gtaagtctaattactttgtttggcctcaattaatttgggttggttagttaacaattg-ttaat--gactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
| | ||| ||| || | || | | || | || | | |||| ||| | |||| ||||| | |||||||| ||| | ||||| ||||| ||||||||||| || || ||||| || ||||||||||| || ||||| ||
gtcgcgaggaagggacgtggattccgcgagtgacaattcggggtatggtgcttccttttgctttcttttttatatttttctctattgttcttcgactaatctattcatcagTGTTGGAAGGCTGGTGGAGAAGTTCAAGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttggcctcaattaatttgggttggttagttaacaattgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
tgttaat putative branch site (score: 3)
ttaacaattgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctaattactttgtttggcctcaattaatttgggttggttagttaacaattgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG