Sequence
atgc intronic sequence ATGC exonic sequencegtatttttttttctcaagtttaactctcgcgcttttggtgtccaaatccttgaatattggtttctcattctctgctactttcaccagGACCATGTTGAAGGATACCTTGAGTTATCAGGCAAAACGAAAACATATTTTTCTACAGCTGTTTCGAAGTGGGATGCAGAGTTCTATGTCAAAGTAGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32430.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os06g46570.2 (Oryza sativa), 3'ss of exon 6
-------------------------------------------gtattttttttt-ctcaagtttaact-ctcgcgct-tttggtgtccaaatccttgaatattggtt--tctcattctctgctactttcaccagGACCATGTTGAAGGATACCTTGAGTTATCAGGCAAAACGAAAACATATTTTTCTACAGCTGTTTCGAAGTGGGATGCAGAGTTCTATGTCAAAGTAGATG
|| ||||| |||| ||| | | || || |||| | || | | | || | | ||| || | |||| ||||||||||||||||||||||||| || || |||||||| || ||||| ||| ||||||||||||| |||||||| || |||||||| || || || |
gtaatattctgcttatgtggtttacgaagaactagctgctccattacctttttgaactcatgttggagtactttcgaagtttgaacttcataccttattgctgtgcctaatgtcagtcctgtccacttctgttagGACCATGTTGAAGGATACCTTGAATTGTCTGGCAAAACCAAGACATACTTTGCTACAGCTGTTTCTTTATGGGATGCTGACTTCTATGTGAAGGTTGACG
upper sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 7
-------------------------gtatttttttttctcaagtt-taactctcgcgcttttggtgtcc---aaatccttga-------atattggtttctcattctctgct-----actttcaccagGACCATGTTGAAGGATACCTTGAGTTATCAGGCAAAACGAAAACATATTTTTCTACAGCTGTTTCGAAGTGGGATGCAGAGTTCTATGTCAAAGTAGATG
|||| |||||| | || | || | || | | |||| || || | | || ||| || ||||| ||||| ||||||||||||||||||| |||| |||||||| || ||||| ||| |||| |||||||| |||||||||||| || ||||| || || ||||
gtaagacaagcacttgcttaattgcttattggtttttcatggatcgtatttatcaagtgactgtttctcctagaatcactgggaatgctatttcgcccccttatttattgtggtctaactttattcagGATCATGTTGAAGGATACCTTGCACTATCTGGCAAAACCAAGACATACTTTGCTACGGCTGTTTCATTGTGGGATGCAGACTTTTATGTGAAGGTTGATG
upper sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 5
-------------gtatttttttttctcaagtttaactctcgcgcttttggt----------gtccaaatccttgaatattggt-----ttctcattctctgctactttcac---cagGACCATGTTGAAGGATACCTTGAGTTATCAGGCAAAACGAAAACATATTTTTCTACAGCTGTTTCGAAGTGGGATGCAGAGTTCTATGTCAAAGTAGATG
| || | || | || | | | | | | || || | || | || | || | ||| || | || | | ||| ||||| ||||||||||| ||||||| || ||||||||||| || || || ||| ||||||||||||| ||||| || || || ||||| || || || |
gtaagttaattccttgttgctcttgcgcaggagtgatacatgtgaactttgttctgagttttgctcagacggctgggttttcctccatattcacagtggctacaatttttttgttcagGATCATGTTGAAGGGTACCTTGCATTGTCAGGCAAAACCAAGACCTACTTTGCTACAGCTGTTTCACTATGGGACGCCGACTTTTATGTTAAGGTTGACG
upper sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G007185_T01 (Zea mays), 3'ss of exon 6
--------gtattttttttt---ctcaagtttaactctcgcgcttttggtgtccaaatccttgaatattggtttctcattctctgctactttcacc--agGACCATGTTGAAGGATACCTTGAGTTATCAGGCAAAACGAAAACATATTTTTCTACAGCTGTTTCGAAGTGGGATGCAGAGTTCTATGTCAAAGTAGATG
|| | | | || ||||| || || | | || | || | | | | || ||| | |||| ||||||||||||||||||||| | ||||| ||||| | ||||| ||| | ||||||||| | |||||||| | |||||||| || || || |
ttcttacaagatccatatatggactgtagttttggggtcattattactttctacatgttttttttcactctaactttagtcatgtgcactcggattgtagGATCATGTTGAAGGATACCTTGAGCTGTCAGGGAAAACCAGGACATACTTTGCAACAGCTGTTGCTTTATGGGATGCTAACTTCTATGTGAAGGTTGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggtgtccaaatccttgaatattggtttctcattctctgctactttcaccagGACCATGTTGAAGGATACCTTGAGTTATCAGGCAAAACGAAAACATATTTTTCTACAGCTGTTTCGAAGTGGGATGCAGAGTTCTATGTCAAAGTAGATG
tttctcattctctgct CT-rich tract
ttgaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttttttttctcaagtttaactctcgcgcttttggtgtccaaatccttgaatattggtttctcattctctgctactttcaccagGACCATGTTGAAGGATACCTTGAGTTATCAGGCAAAACGAAAACATATTTTTCTACAGCTGTTTCGAAGTGGGATGCAGAGTTCTATGTCAAAGTAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT