Sequence
atgc intronic sequence ATGC exonic sequencegtgtgttcttaggaaacaaatgaagcatgttggctacatgaaactacaaaattcggattcttctccatttgttctatgtactgacttggacctgcattttctatttcagGAGAAATGGGCGAAAAATCTGTACATTGCATCAATATGCTATGGTCGGACAGTTTGCTGATGAAACATGGAGTATACTGTTTCAACCTCTCTCACTCTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03940.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os01g56580.1 (Oryza sativa), 3'ss of exon 16
---------------------------gtgtgttcttaggaaacaaatgaagcatgttggctacatgaaactacaaaattcggattcttctccatttgttctatgtactgacttggacctgcatt----ttctatttcagGAGAAATGGGCGAAAAATCTGTACATTGCATCAATATGCTATGGTCGGACAGTTTGCTGATGAAACATGGAGTATACTGTTTCAA-CCTCTCTCACTCTCT
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gtacgaatacatgactaattcctgtgtacattgtttttcttcacagttctctctaaccagaccattcaacttacatttcttgttcaagcgtcaactcgatcactactctaaccttgtcccatactgttgtctttttgtagGAGAAATGGGCCAAGAATCTTTACATTGCTTCGATATGCTATGGCCGGACAGTATCTTGA-GGCATACCCTGCACACCAACTCGGGCTTAGCATATTCGCA
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 16
gtgtgt---tcttaggaaacaaatgaagcatgttggctacatgaaactacaaaattcggattcttctccatttgttctatgtactgacttggacctgcattttctatttcagGAGAAATGGGCGAAAAATCTGTACATTGCATCAATATGCTATGGTCGGACAGTTTGCTGATGAAACATGGAGTATACTG--TTTCAACCTCTCTCACTCTCT
|| | | | | | | | |||| | | | || || | ||| ||| || | || | | | | || | | || | | | | | ||||| ||||||||||||||||||||||| ||||| || |||| || || || || || ||| | | ||| || || | | |
gtatatacattatcgcagctcattgaaatccggccgtgtcttgtaaaaaacaaacata-atttctcgcgtttcgga--gttcagtaacatag-ccggtgtgctgt-tcgcagGATAAATGGGCGAAAAATCTGTACATAGCATCGATCTGCTTCGGGCGAACCGTCTGTTGACGGTGTGGCTGGCTGGCTGCCTTCCATTGAAGTTGAAGCG--
upper sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 16
gtgtgttcttaggaaacaaatgaagcatg-ttggctacatgaaactacaaaattcggattcttctccatttgttctatgtactgacttggacctgcattttctatttcagGAGAAATGGGCGAAAAATCTGTACATTGCATCAATATGCTATGGTCGGACAGTTTGCTGATGAAACATGGAGTATA---CTGTTTCAACCTCTCTCACTCTCT
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------------------------gtatgatcatatatttgtatccttgaccgcgctgtttcaaatcacccatttaacgtcgacaaaataatctggatcttttg---cagGAGAAATGGGCCAAGAACCTTTACATTGCTTCAATATGCTATGGCCGGACAGTGTCATGAGGCTTGCTCGGCTGCATCCCTAGTTGGGAAGAGCATGTTC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggattcttctccatttgttctatgtactgacttggacctgcattttctatttcagGAGAAATGGGCGAAAAATCTGTACATTGCATCAATATGCTATGGTCGGACAGTTTGCTGATGAAACATGGAGTATACTGTTTCAACCTCTCTCACTCTCT
tactgac putative branch site (score: 1)
ttttctatttc putative PPT
attttctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttcttaggaaacaaatgaagcatgttggctacatgaaactacaaaattcggattcttctccatttgttctatgtactgacttggacctgcattttctatttcagGAGAAATGGGCGAAAAATCTGTACATTGCATCAATATGCTATGGTCGGACAGTTTGCTGATGAAACATGGAGTATACTGTTTCAACCTCTCTCACTCTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA