Sequence
atgc intronic sequence ATGC exonic sequencegtaatatctcctctttgcttcccttgctgcctatttttagatctgacattgtcaaaagtagttattgtacactgagttcatctacaagagtggtttatttaagtcattgtttatgcttcagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G02010.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G02010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g14932.1 (Oryza sativa), 3'ss of exon 5
--------------gtaatatctcctctttgcttcccttgctgcctatttttagatctgacattgtcaaaagtagtt----attgtacactgagttcat-------ctacaagagtggtttat--------ttaagtcattgttta--------tgcttcagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
|| | | | | || ||||||| || || || | || || || || ||||| | | | || | | || || | | || |||| || || | |||||| | | || | | | || | || |||||||| ||||||| ||| ||||| |||||||| || ||| | |||||||||||||| || || || ||
gtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcagGTACATTGGGAGCTAGCCGCCCCTTGGACTGGGACACTAGAATGAGGATAGCACTAGATGCTGCCAGGGGATTGGCATACCTTCATGAGGATTCTCAGCC
upper sequence: AT4G02010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g14932.3 (Oryza sativa), 3'ss of exon 6
--------------gtaatatctcctctttgcttcccttgctgcctatttttagatctgacattgtcaaaagtagtt----attgtacactgagttcatc-------tacaagagtggttta--------tttaagtcattgttta--------tgcttcagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC----------------
|| | | | | || ||||||| || || || | || || || || ||||| | | | || | | || || | | || |||| || || | |||||| | | || | | | || | || |||||||| ||||||| ||| ||||| |||||||| || ||| | |||||||||||||| || || || ||
gtatggccaattgagtcaactatttctccttctgaaattgctgcataagttccactcagttgcagttgaatgtggtccttcattgtttaattaattagtggtgatcatgtaatcatgatacaccttgactcttgagtctctgactacttacatttttttcaggtacattgggagctagCCGCCCCTTGGACTGGGACACTAGAATGAGGATAGCACTAGATGCTGCCAGGGGATTGGCATACCTTCATGAGGATTCTCAGCCTTGCGTAATCCACAGG
upper sequence: AT4G02010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G37910.1 (Glycine max), 3'ss of exon 6
--------------------gtaatatctcctctttgcttcccttgctgcctattt--ttagatctgacattgtca-aaagtagttattgta---cactgagttcatctacaagagtggtttatttaagtca---ttgtttatgctt--cagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
| || || || || | || | | | || || | ||| |||| | | ||| ||| | || || | | | | | | | | | || || ||| || ||| |||| || | || | || |||||| | |||||||||||||||||||||||||| |||||||||||||| |||||| ||||||| ||||||||||| || ||
gtaatgtaatttttcgaatcatgggttcagcttttagcattgtatggtacatgctttctttgttctattattgacttattgtacttagtatagttttctcaatgtgtgttttat-gccttaaactgaaatcggccttgattttgcccggcagGTCCCTTGGGAATCAATTGTCCTTTGGATTGGGACACCAGAATGAAGATTGCGCTTGATGCTGCAAGGGGACTTTCATACCTGCATGAAGACTCACAGCC
upper sequence: AT4G02010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G01520.1 (Glycine max), 3'ss of exon 4
--------------------gtaatatctcctctttgcttcccttgctgcctatttttagatctgacattgtcaaaagtagttattgtacactgagttcatctacaagagtggtttatttaagtcattgtttatgcttcagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
| | | |||| | | | | | ||||| ||| || || | | || | | || || | | | | | | || | | | | | |||| | || ||| || || || | || || || | ||||||||||| ||||||||||| || ||||||||||||||||||||||||||||| |||||||| || || ||
gtaatataatttctcaaatgatggcaccagctctgtaatcttgaaattacatgtttttct-tcttccaa-gtttacaataatgttggttcagaaactattttattatgcttaattgaaattggccttggtttttcct--agGTCCCCTGGGAATAAATTGCCCCTTGGATTGGGACACTAGAATGAAGATCGCCCTTGATGCTGCAAGAGGACTTGCATACCTGCATGAAGATTCACAGCC
upper sequence: AT4G02010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G40500.1 (Glycine max), 3'ss of exon 5
--------------------gtaatatctcctcttt-gcttcccttgctgcctattttt--agatctgacattgtca-aaagtagttattgta---cactgagttcatctacaagagtggtttatttaagtca---ttgtttatgctt--cagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
| | || || ||| || | || | | | ||||| | ||| |||| | | || ||| | || || | | | | | | | ||| || || ||| || || |||| || | || | ||||||||| | |||||||||||||||||||||||||| || |||||||| || |||||| ||||||| ||||||||||| || ||
gtaatggaattttccgaatcatggtttcagctttttagcattgaatgttacatgttttttttgttctattattgacttattgttcttagtatagttttctcaaaacgtgttttat-gccctaaattgaaatcggccttgatttggcccggcagGTCCCTTGGGAATCAACTGTCCTTTGGATTGGGACACCAGAATGAAGATTGCGCTGGATGCTGCGAGGGGACTTTCATACCTGCATGAAGACTCACAGCC
upper sequence: AT4G02010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G01480.1 (Glycine max), 3'ss of exon 4
-----gtaatatctc--ctctttgcttc--ccttgctgcct---atttttagatctgacattgtcaaaagtagttattgtacactgagttcatctacaagagtggtttatttaagtcattgtttat--gcttcagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
|||| |||| || | || || | || || | | | | | | | || ||| | || | || | | | ||| || ||| || | || || | ||| || || || | || || ||| | ||||||||||| ||||||||||| || ||||||||||||||||||||||||||| | |||||||| || || ||
gtaatataatttctcaaatcatggcatcagctctgtaatcttgaaatgacatgttttgcttcttccaaatttacaataacgt-ttaagaaagtattttactgtgcttaattaaaattggccttgatttgtcctagGTCCGCTGGGAATAAATTGCCCTTTGGATTGGGACACTAGAATGAAGATCGCCCTTGATGCTGCAAGAGGACTTGCATACATGCATGAAGATTCACAGCC
upper sequence: AT4G02010.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g01590.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------gtaatatctcctctttgcttcccttgctgcctatttttagatctg-acattgtcaaaagtagtta----ttgtacactgagttcatctacaaga-gtggt-ttatttaagtcattgtttatgcttcagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
| |||| | | ||| || | | |||||| | | || | ||| |||| | | ||||| | | || | ||| | | || || | | |||| |||| |||| ||||| || | ||||||||| | |||||||||||| ||||||||||||| ||||||||||| ||||| ||||||||||| ||||| || || |||||
gtagtttgctttcttgaaccacagatttaatgaaatcctcatatatttatctctctttccattgtccctattatggattgtgtatcttggaaaaaaatataaaactctgtacttttgggagattttcaatacatagtattgacaatggtcctgttc-tgctccagGCCCTCTGGGAGTCAACTGTCCTTTGGATTGGGACACCCGAATGAAGATTGCTCTTGATGCTGCCAGAGGGCTTGCATACCTGCATGAGGATTCACAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacactgagttcatctacaagagtggtttatttaagtcattgtttatgcttcagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
tttatttaagtcattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatatctcctctttgcttcccttgctgcctatttttagatctgacattgtcaaaagtagttattgtacactgagttcatctacaagagtggtttatttaagtcattgtttatgcttcagGGCCTCTCGGGTTGAACTGTCCTCTTGATTGGGACACCAGAATGAAGATTGCACTTGATGCTGCAAGAGGACTTGCATACCTTCATGAAGACTCGCAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA