Sequence
atgc intronic sequence ATGC exonic sequence...gtcgtcacattctcatgcaattctaccatttgaattattcaagattgttcctttacaatgtgtctaatgtatgttatgttttgataaaaaataatcgcagGGGCTCACCGAGAAGTTCAAGGAGAAGGATACGGCGTTATCAGGCTCAGCTATTTTCAATTACGAGAACTTCATGCTCACTGTTTTACCATTCCTCGTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G10300.4 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G10300.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G357595_T01 (Zea mays), 3'ss of exon 4
------------gtcgtcacattctcatgcaa-ttctaccatttgaa-----ttattcaagattgttcct----------ttacaatgtgtctaatgtatg-ttatgttttgataaaaaataatcgcagGGGCTCACCGAGAAGTTCAAGGAGAAGGATACGGCGTTATCAGGCTCAGCTATTTTCAATTACGAGAACTTCATGCTCACTGTTTTACCATTCCTCGTCG
| | ||| | ||||| || ||||||| || | || | || || | |||| | ||| | | || | || ||| | | | ||||||||||| || |||||||||||||||||||| || || | || || || || | ||||| |||||| ||||||||| || || | || |||||| | |
gtaactaataacgcctgcactgtagtgtgcaaactcgaccatttcaaactttctctttgcgtctgatcttgcaaatgcagttacgaacgatcttacctgtggtcattgttttttggatcact-tcgcagGGGCTGACAGAGAAGTTCAAGGAGAAGGACACCGCCTACTCTGGGTCGGCGACTTTCACCTACGAGGCCTTCATGCTGACCGTGCTGCCTTTCCTCATTG
upper sequence: AT3G10300.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ19099 (Selaginella moellendorffii), 3'ss of exon 3
gtcgtcacattctcatgcaattctaccatttgaattattcaagattgttcctttacaatgtgtctaatgtatgttatgttttgataaaaaataatcgcagGGGCTCACCGAGAAGTTCAAGGAGAAGGATACGGCGTTATCAGGCTCAGCTATTTTCAATTACGAGAACTTCATGCTCACTGTTTTACCATTCCTCGTCG
| | | | | ||| | || | ||| ||| | | | | || | ||| || ||| |||||| ||||| ||||||||||||||||||||| | | | | ||||| || | | | |||||| |||||||| | ||||| || ||| | || |
----------------gtgagttcatcgttttattttct--------ttcttttgttgttttggtgacac-tgacaagttcc--taccgtgcaat-gcagGGACTCACGGAGAAGTTCAAGGAGAAGGATGTGAAGCTCACGGGCTCGGCCACGCTAAGCTACGAGGCGTTCATGCTTATGGTTTTGCCTTTCATTGTTG
upper sequence: AT3G10300.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ22574 (Selaginella moellendorffii), 3'ss of exon 3
gtcgtcacattctcatgcaattctaccatttgaattattcaagattgttcctttacaatgtgtctaatgtatgttatgttttgataaaaaataatcgcagGGGCTCACCGAGAAGTTCAAGGAGAAGGATACGGCGTTATCAGGCTCAGCTATTTTCAATTACGAGAACTTCATGCTCACTGTTTTACCATTCCTCGTCG
| | | | || || | || | | ||| ||| | | | | || | ||| || ||| |||||| ||||| ||||||||||||||||||||| | | | | ||||| || | | | |||||| |||||||| | ||||| || ||| ||
----------------gtgagttcatcaattcatcgttttattttctttcttttgttgttttggtgacac-tgacaagttcc--taccgtgcaat-gcagGGACTCACGGAGAAGTTCAAGGAGAAGGATGTGAAGCTCACGGGCTCGGCCACGCTAAGCTACGAGGCGTTCATGCTTATGGTTTTGCCTTTCATC---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcctttacaatgtgtctaatgtatgttatgttttgataaaaaataatcgcagGGGCTCACCGAGAAGTTCAAGGAGAAGGATACGGCGTTATCAGGCTCAGCTATTTTCAATTACGAGAACTTCATGCTCACTGTTTTACCATTCCTCGTCG
taatgtatgttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcgtcacattctcatgcaattctaccatttgaattattcaagattgttcctttacaatgtgtctaatgtatgttatgttttgataaaaaataatcgcagGGGCTCACCGAGAAGTTCAAGGAGAAGGATACGGCGTTATCAGGCTCAGCTATTTTCAATTACGAGAACTTCATGCTCACTGTTTTACCATTCCTCGTCG
- - -cacattc
- - - - - - tcatgca
- - - - - - - - - - -tctacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa