Sequence
atgc intronic sequence ATGC exonic sequencegttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G16540.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 6
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
||| | | | | | ||| | | | | || | | | || | | | || | | || | || | | ||| |||||||| || | ||| ||||||||||| ||||| ||||||||||||||||| | || ||||||||||| || ||| || | | || |
gtttatcatgcaatgttcaaaaccga-taaaacataaatacatacaatatagaagatggacaagtgttgcctaatcctctgtttctttttcctgcttg---cagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGTCCGAATTGCAAATTTGATCATCCAATGGGAACTGTGATGTATGGTCTCG
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g21700.1 (Oryza sativa), 3'ss of exon 6
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
| |||| || ||| | | || | || | | ||| | || || | ||| ||| | | | ||||||||||||| | ||| ||||||||||| || |||||||||||||||||||| | || |||||||| || || ||| || | | | || |
--agtagttccaataaatt--ataatacttgagtaatctgtaatttggtactttttgcctatcgggggatgctaccctaacatctatctctttcctgctaacagGGAGAACCTGTCTGCACATTCTATTCTCGTTACGGGATCTGCAAGTTTGGTCCTAATTGCAAATTTGACCATCCTATGGGAACCCTTATGTATGGAAGTG
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 5
gttggccttcctt-tacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-
|| | | || | ||| |||| || | |||| || | | | | || || || | || | | | | ||| ||||||||| ||||||| |||||||||||| ||||| ||||||||||| || | | || |||||||| || || | | | || | | | |
actgtatatattagtatgaagattaacacttgaaaaaacctttgattgttcctataaca-cctaatgattgactatgacacggctgtttcgagatttt----cagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGG-CTCCTCCAATGGGAGTGT
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 6
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggta----aattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-
| | ||| | | |||| ||| | || ||| || | |||||| |||| || | ||| | | | | |||| ||| ||| ||| ||||||||||| ||||| ||||||||||| || | | ||||||||||||||| || | | || | | | |
------tacaaataaagcctgtctcacgaataggc-actagctagtccttctggtaca-cctcattgaatggtctgccatcttgattatcctgtccaatggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGCGCCAACTGTAAATTTGATCATCCTACAATGG-CTGCTCCAATGGGAGTTT
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 6
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-
| || | | | ||| | | | | | ||| ||| || || || || || | || | | | | ||| ||||||||| || ||||| ||||||||||| || ||||| || ||||| |||||||||||||| || ||||||||||| ||| |||||||||| || ||||
gatgagaatatatgcaattcagtattgtcttcacactgatttgatatttttattgat---ttcggtacatg--ctaatagaggttgtgtcccattttcctacaggGAGAGCCCCTGTGTGTGTTCTATTCACGTTATGGCATATGCAAATTTGGTCCAAGCTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATGTC
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 6
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggt--ttggtaaattcttgt-tgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
| | || | | || || | |||| | | | | | || || | | | | |||| | | ||| ||||||||| || ||||| ||||||||||| || || || || ||||| ||||||||||| || || ||||||||||| ||| |||||||||| || ||||
agggagatgagaatatatgcaattgtttattacagtg-------ttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G31370.2 (Glycine max), 3'ss of exon 5
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcatta-tgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
| ||| | | | | | | | | | | || | | |||| || | || || | | || | ||| |||||||||||| |||| || ||||||||||| ||||| || ||||| ||||| ||||| || || ||||| ||||| ||| | | ||| || | || | |
----acaaatatttgtgttttttttttttttcacgttagtttggtcttgtgagttgtgattgaattagtgcaatctgatagaggca-gtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 6
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcatta-tgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
|| | | | | ||| | | | | | || | | |||| || | || || | | || | ||| |||||||||||| |||| || ||||||||||| ||||| || ||||| ||||| ||||| || || ||||| ||||| ||| | | ||| ||||||| | ||
-caaatatttgtgggttttttttctcttcacgttagatt---ggtcttgtgtgttgtgattgaattagtgcaatctgatagaggca-gtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTTACAATATCA
upper sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
| | | | | | || | | | | | || ||||| | |||| |||| | || || ||| | ||| ||||||||||||| ||||| | || |||||||| |||||||||||||| ||||||||||| || || ||||| ||||| ||| || ||||| | |||||
accataatgcataaatgtacttcaactt--tggttgctctgatatagagtccttgtctagttatttata-aatttgatggat-ctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
taaattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggccttcctttacgcccggtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG