Sequence
atgc intronic sequence ATGC exonic sequencegtactacttatactcattcatttcatgtgctaccagattttctgattttctctggttttatgaatcttgaaattgctgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G60100.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
------------------gtactacttat-actcattcatttcatgtgctaccagattttctgattttctctggttttatgaatcttgaaattgctgta-----tcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
| || |||| ||| || | || | | ||| || | | || ||| | | ||| ||| | || | ||||||||| ||||| |||||||| ||||||||||| |||||||| || |||||| ||| ||| || | ||||| |
gtaatgctactagattgatcaataattattgctcctttaattacggctccttcagtttacttccatctcattggct--aagaaataagaacatccttcacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
gtactacttatactcattcatttcatgtgctaccagattttctgattttctctggttttatgaatcttgaaattg-ctgtat---cagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
||| | | || ||| || ||||||| || | | | | ||| | | | | | |||| | ||| |||||||| ||||| |||||||| ||||||||||| || ||||| || |||||| ||| ||| || | ||||| |
gtaatgccactag--attgatcatgattgctaccgttttatgtccatcttattggctaaa-aagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
gtactacttatactcattcatttca-tgtgctaccagattttctgattttctctggttttatgaatc-----ttgaaattgctgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
||| | | ||| || || | | || || | |||||| | | | ||| || | | ||||||||||||||||||||| || ||||||||||| || ||||| | |||||| ||| ||| ||| | |||||| |
gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 3
-----------gtactacttatactcattcatttcatgtgctaccagattttctgattttc-tctggtttta----tgaatcttgaaattgctgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
| | | ||||| || | |||||| || | | || ||||| | | | ||| || | | ||||||||||||||| ||||| || ||||||||||| || ||||| | |||||| ||| ||| ||| | |||||| |
cttcttaagaatttttttccaatctcatccaatccatgtgtattgggaataaccgaacaaagcctggtgtgaacactattctttgcccatgttttctcagGTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 17
------------------gtactacttatactcattcatttcatgtgctaccagattttctgattt-tctctggttttatgaatcttgaaatt--gctgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
|| | | |||||||| | || || ||| || || | |||| | ||| | | | ||||| || || |||| || || || |||||||| ||||||||||| || |||||||| |||||||| ||||||||||| || | ||
tcatacacattaaaccggataacagatgtactcattgctctcttg--ctattag---ttgtaatttattcctgatacgactgaacttgagttttaaatggtgtagGTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAA
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 17
------------------gtactacttatactcattcatttcatgtgctaccagattttctgattt-tctctggttttatgaatcttgaaattgc--tgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
|| | | |||||||| | || | || || | | |||| | ||| | | | ||||| || | | |||| || || || ||||| || |||||||| || || |||||||| |||||||||||||||||||| || | ||
tgatacacattaaaacggataacagatgtactcattgctctctaga--tattag---tcataatttattcctgatacgactgaacttgagttttcaacggtgtagGTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAA
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------gtactacttatactcattcatttcatgtgctaccagattttctgattttctct---ggttttatgaatcttgaaattgctgt-atcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
|| | || | | ||| | | ||| | || ||| | | | || ||| | || | || |||||||||||||||| |||||||| || |||||||| ||||| || || || | ||||| || | | ||| |
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattttgaagtcttacttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: EFJ29959 (Selaginella moellendorffii), 3'ss of exon 16
gtactacttatactcattcatttcatgtgctaccagattttctgattttctctggttttatgaatcttgaaattgctgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
| || || || | |||| | | | | ||||| || || || ||||||||||| ||||| ||||||||||||||||| | |||| || | || |||| |
-----------------------------------------gtaatactcgctattcacggcaatcataatgccccccttccagGTGAAAAATCCTTGGCCTAACGTGGATGCGCATAGCGGAGTGCTTCTACAATACTTCGGGTTGACTGAAGAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaccagattttctgattttctctggttttatgaatcttgaaattgctgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
ttctgat putative branch site (score: 3)
ttttatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactacttatactcattcatttcatgtgctaccagattttctgattttctctggttttatgaatcttgaaattgctgtatcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG