Sequence
atgc intronic sequence ATGC exonic sequence...attcaatagttctgttcgtgttgcccttgaagccgatatatttataagagctgctccaattgtgtcatttcctaacaattatcaagtttacttgccgcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 5
attcaatagttctgttcgtgt-tgcccttgaagccgatatatttataagagctgctccaattgtgtca----tttcctaacaattatcaagtttacttgccgcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
|| | || | ||| | | |||| || | ||| | | || | | | | || | ||| | || | || ||||||||||| |||||||| || || || || |||||||| ||||| |||| ||||| ||||||||||| ||||| ||||| || ||||||||||| || |
-ctctcttttttt-ttcatatatgccattt--gttattatttatgcaaatatccatttatgtattccagatgatcccttattccctcatggtgtttttatt-cagAATGTCAAGACATTTAAAGATGTCAAAGGGTGTGATGACGCAAAGAAAGAACTCGAGGAGGTAGTTGAGTATCTAAAAAACCCTTCAAAGTTTACTCGGC
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------attcaatagttctgttcgtgttgcccttgaagccgata-tatttataagagctgctccaattgtgtcatttcct---------aacaatta-----tcaagt-----ttacttg---ccgcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
| ||| | | || ||||| ||| | ||| | | | | | | | ||| ||||| ||||| || |||| | || || ||||||||||| |||||||| || || || |||||||||||||||||| | || || || ||||||||||| |||||||| || || |||||||| || ||||
gtatctgattacgcttcataaaatacttgatacaagagtatcttggtccactttgggttactacaaaaacattattagtgtttttctttcgcacaatactgtcttctggttgtctgttagtaatgtgatttctcggtacagaaaacaaatacatattcaaatgataattctatggttttacagAATGTCAAGACATTTAAAGATGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAGGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCC
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------attcaatagttctgttcgtgttgcccttgaagccgata---tatttataagagctgctc--caattgtgtcatttccta---------acaatta-----tcaa--gtttacttgccg---cagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
| || | | | || ||||| |||| | ||| | ||||| | || | || | ||| ||||| | |||| || |||| | || ||| | ||||||||||| |||||||| || || || |||||||||||||||||| | || || || || |||||||| |||||||| || || |||||||| || ||||
gtatctgagtacgcttcataaagtacttggtgcaagaagagtatcttggtccattttgggttactacatgaactttattagtgttttccttctgcaccatactgtctttattgctgttgtttgacagtaatgtgatttctcagtacagaaaacaaatacatattcaaatgcttctatgctgtttcagAATGTCAAGACATTTAAAGATGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAAGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCC
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 5
attcaatagttctgttcgtgttgcccttgaagccgatatatttataagagctgctccaattgtgtcatttcctaacaattatcaagtttacttgcc--gcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
| | || ||| | | || || | | | | | || | | | || ||||| || ||| || ||||||||| ||||| |||||||| || || ||||||||||||||||| ||||| || || || || || || || || ||||||||||| |||||||| ||||
-cttagcc-ttgtgtgtagaatatacagtaaaccaaaagttcttctacgccttatgtgctcacttttcttatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 5
attcaatagttctgttcgtgttgcccttgaagccgatatatttataagagctgctccaattgtgtcatttcctaacaatt----atcaagtttacttgcc--gcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
| | || ||| | | || | | | | | | | || | | || |||| ||| || |||| || ||| || ||||||||| ||||| |||||||| || || ||||||||||||||||| ||||| || || || || || || || || ||||||||||| |||||||| ||||
---ttagacttgtgtgtagaatatacagtaaatcaaaagttcttccacatcttatgtgttc---tcttttcttaatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 5
attcaatagttctgttcgtgttgcccttgaagccgatatatttataagagctgctccaattgtgtca--tttcctaacaattatcaagtttacttgccgcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
| | || | | | | || ||| | || | | |||| || || ||| | | | | | || | | ||||||||| ||||||||||| || || || |||||||| |||||||||||||| || || || || || ||||| || ||||||||| | || ||||||||||
-ctgattacacacacacactcacacatacagagagaccaattgacaacaaatcagaaaattatgacaaacaaccttata-taagctctctttcctcttgcagAATGTTAAAACATTTAAAGATGTGAAAGGTTGTGACGATGCAAAACAAGAACTTGAGGAAGTTGTGGAATACCTGAAAAATCCAGCTAAATTTACCCGCC
upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------------------------------------------attcaatagttctgttcgtgttgcccttgaagccgatatatttataagagc-tgct--ccaattgtg---tcatttcctaacaattatcaagtttacttgccgcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
||| | |||| | ||| | | | | || | ||| | ||| ||| |||||| || | | | | | | |||| ||||||||| || ||||||||||| || || || ||||||||||||||||| ||||| || || ||||| || || |||||||| || |||||||||| | |
gtagatatctgatgttacgtgttttgtattatatgttttaagagtgtttctggagatttcaagtctattgagcaagttgtgcaagtgatttag-agttgtattcattt---catatggaccatcctgttttttgaagcatgccagttaattgtagtcctgttatttttctctgagtagttgcctttgctgcagAATGTTAAGACATTTAAGGATGTGAAAGGCTGTGATGATGCAAAACAGGAGCTTGAGGAAGTAGTGGAGTACCTCAAAAACCCTGCAAAGTTTACTAGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagagctgctccaattgtgtcatttcctaacaattatcaagtttacttgccgcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
tcctaac putative branch site (score: 1)
tttactt putative PPT
aattatcaagttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcaatagttctgttcgtgttgcccttgaagccgatatatttataagagctgctccaattgtgtcatttcctaacaattatcaagtttacttgccgcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - ctgctcc