Sequence
atgc intronic sequence ATGC exonic sequencegtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08530.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 10
--gtatgcgatgtttatcatggatctgttgtctcggtgaagtaatta-----tatagttgttaa--atggcagcttgaagaa-aaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
| | || | ||| | |||||| | || |||| || |||||| ||| | || | | | || | | | | | | | | | || | || ||| ||||||| || |||| || || ||||| || |||||||| |||||||| || |||||| | ||||| |||||||||||||| |||| | || |||||||
gtaagttccattacttctatgcttttgttgtgatgctgttacaattgcaatttacgcttgttacctatgctggttttatcagtggcatatattttcctgcaagatatgatagcgagtttaatgtttt-atattgcagGTTGTGCAAAGGTTTCAAGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGATA
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 10
--gtatgcgatgtttatcatggatctgttgtctcggtgaagtaat-----tatatagttgttaa--atggcagcttgaagaa-aaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
| | || | ||| | |||||| | || ||| | || |||||| ||| | || | | | || | | | | | | | | | |||| || ||| ||||||| || |||| || || ||||| || |||||||| |||||||| || |||||| | ||||| |||||||||||||| |||| | || ||||| |
gtaagttccattacttctatgcttttgttgtgatgctgttacaatcgcaatttacgcttgttacctatgctggttttatcagtggcatatattttcctgcaagatatgatagcgagtttaatgcttt-atattgcagGTTGTGCAAAGGTTTCAAGAATTGTTTGCACAAACAAAATACAAGGAAGCAGCTGAGTTGGCTGCAGAATCTCCTCAAGGTCTTCTCCGAACTCCTGAGA
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 10
gtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
|| || ||| | | ||| || | | | ||| || || | || | | ||| | | ||| || |||||| || | || || |||| || | || || || || |||| || |||||||| || ||||| ||||| |||||||| ||||||||||| |||||||| || | || ||||| |
--------tgattgctatg--tttagcttcttaagaaatgctctctcttgttattgtatttttggttc-----------ttttattcatgaatatgatgtc---catatt-tgtt--gacattacagGTAGTGGAACGTTTTCATGAACTGTTTGCCCAAACAAAATATAAGGAAGCTGCAGAGCTTGCAGCTGAATCTCCACAAGGAATCCTTCGAACTCCTGACA
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 10
gtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatat-tctgctcg--gatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
|| | | | ||| | || ||| | | ||| ||| || |||| ||| ||| || | || || | | | || || | || || |||| || | || ||||| || |||| || ||||| ||||| || || || ||||||||||||||||| ||||| |||||||| || | ||||||||||
----------------gtgtgta-atagcctcatttaa--aatggtttcgttttta--tgattgctttgt---------tgttgttttgtgtattgtagccattaacgtgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 10
gtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
|| | | || | || || || || | | ||| | | ||| | | | | | || || | | || || || |||| || | || ||||| || |||| || ||||||||||| || || || ||||| ||||||||||| ||||| |||||||| || | ||||||||||
---------gtgtgtaatagcctcatt--taaaatggtttagtttttttattgctttgtttttttttgtgtgta-----ttttactcattaacatg----cctccttgtt-------gacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
gtatgcgatgtttatcatggatc-tgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
|||||| || | | ||| |||| | | ||||| |||||||| || || || || || |||| ||| | | | | | || | ||||||||||||| ||||| || ||||| ||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||| | ||||| || |
----------agaatcatgtttcatatagtcatggtggaa-atttatac---tgttaaat--cattatgtag----------tctttgcatatttggaatctgatagcctgccatttctatatc--agGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 10
gtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
| | | | ||| ||| ||| | | | | | | | || ||||||||| || ||||| |||||||| ||| |||| |||||||| || ||||| |||||||| ||||| || ||||||||||| || | || | ||| |
------------------------------------------------------------gtaacgcttttatcttcgatgatctttctctttgctacctcttac-tgtatcgttctatgtgagtagGTTGTGCAACGGTTTCAGGAGTTATTCCAACAAATGAAGTACAAAGAAGCTGCGGAGCTTGCAGCTGAGTCCCCTCAAGGAATCCTTCGCACGCATGACA
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 10
gtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
| | | | ||| ||| ||| | | | | | | | || ||||||||| || ||||| |||||||| ||| |||| |||||||| || ||||| |||||||| ||||| || ||||||||||| || | || | ||| |
------------------------------------------------------------gtaacccttttatcttcgatgatctttctctttgctacctcttac-tgtatcgttctatgtgagtagGTTGTGCAACGGTTTCAGGAGTTATTCCAACAAATGAAGTACAAAGAAGCTGCGGAGCTTGCAGCTGAGTCCCCTCAAGGAATCCTTCGCACGCATGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
tcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA