Sequence
atgc intronic sequence ATGC exonic sequencegttcgtgccccttcttctcctttgtatcaatctcaatgagtatagtttttgtaattgtggttgaatgtgacacagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G26680.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G26680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G121262_T01 (Zea mays), 3'ss of exon 3
--------------gttcgtgcccctt------cttctcctttg-----tatcaatctcaatgagtatagtttttgtaattgtggttgaatgtgacacagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
| ||||| ||| || || || || || | | | |||| || | | | ||||||||| |||||||| || || | |||| ||||| |||||||||||||||||||||||
attggttgcatgtattccgtgcgtcttgatatgctactactgtgttagttacctactgccatgaaagagcgggacaggtttcttatacttccttgaacagATTGTAGTTGGAAGGACAGGCATGGAAACTCTCACAAATGAAGCTGGTGAAGTCACTAG
upper sequence: AT5G26680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G28200.1 (Glycine max), 3'ss of exon 2
-------------------------------------gttcgtgcccc--ttcttctcctttgtatcaatctcaatgagt--atagtttttgtaatt-gtggttgaatgtgacacagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
|| || | || | | ||| || | ||| | | || ||| ||| || | || | || |||||||| || ||||||| ||| |||||||||||||||||||| ||||||||||| || ||
gtcagtgctaatcttcacaacacatgacgtagtttcaatttcaaccatgatactaatacagtgtgattatgttaataacttaatgtcacatgttatttgtcttggattttggtgcagATTGTCGTGGGAAGAAGTGGAACTGAAATGCTCACTAATGAGGCTGGTGAAGTTACCAG
upper sequence: AT5G26680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G22190.1 (Glycine max), 3'ss of exon 2
-----------------------------------gttcgtgcccc--ttcttctcctttgtatcaatctcaatgagt--atagtttttgtaattgtggttgaatgtgacacagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
|| || | | || | | | || || | ||| | | || ||| |||| | || | || ||||||||||| ||||||| || |||||||||||||||||||| ||||||||||| || ||
gtcagtactaatcttcccaacacagcgtagtttcaatttcaaccacgatactaatacagtttaattatgttaataacttaatgtcacgtgtttttgtcttggattttggtgcagATTGTTGTGGGAAGAAGCGGAACTGAAATGCTCACTAATGAGGCTGGTGAAGTTACCAG
upper sequence: AT5G26680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 2
gttcgtgc-cccttcttctcctttgtatcaatctcaatgagtatagtt----tttgtaattgtggttgaatgtgac---acagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
|| | | |||| || | ||| ||| || |||| || ||| ||||| | || ||| | ||||||||||||||||||| |||||||||||||||||| ||||| ||||| ||||| |||||
gtctgcacattcttcactctctctctatacgtctttttgtatatatttatgatttttaatt-taaatgctcgtgcctttgcagATTGTTGTTGGAAGAAGTGGGACTGAAATGCTCACAAATGAGGCTGGCGAAGTTACTAG
upper sequence: AT5G26680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ19284 (Selaginella moellendorffii), 3'ss of exon 1
gttcgtgccccttcttctcctttgtatcaatctcaatgagtatagtttttgtaattgtggttgaatgtgacacagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
| || || |||| | | | | || ||| || |||||||||| ||| ||||||| |||||||||||||| ||||| ||||| ||| | || ||
----------------gtgagttctagatatctttgcgt-tgtgtctcacacaagaagccttgcattc----tagATTGTTGTGGGACGAACTGGCACTGAAATGCTCACGAATGAGGCTGGAGAAATTACAAG
upper sequence: AT5G26680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ10540 (Selaginella moellendorffii), 3'ss of exon 1
gttcgtgccccttcttctcctttgtatcaatctcaatgagtatagtttttgtaattgtggttgaatgtgacacagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
| || || || || || || | | | | | | | || |||||||||| ||| ||||||| |||||||||||||| ||||| ||||| ||| | || ||
----------------gtgagttcta--gatatctttgcgt-tgcgtctcacacaagaagccg--tgcattctagATTGTTGTGGGACGAACTGGCACTGAAATGCTCACGAATGAGGCTGGAGAAATTACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtatcaatctcaatgagtatagtttttgtaattgtggttgaatgtgacacagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
tatagtttttgtaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtgccccttcttctcctttgtatcaatctcaatgagtatagtttttgtaattgtggttgaatgtgacacagATTGTTGTTGGAAGAACTGGGACTGAAATGCTCACTAATGAAGCTGGTGAAGTCACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG