Sequence
atgc intronic sequence ATGC exonic sequencegtattaagcaattcggatctcagaacttatccaaaactttctgctgcgttttgcgctgcttatactggagtgttttttttcattattggcagAAAAGTATGAGCCGGTCAACGTGAAATGGACAACCGAGCGATGTGCAGTTTGCAGATGGGTGGAAGATTGGGACTACAACAAGATCATTATCTGCAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53430.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 10
gta--ttaag--caattcggatctcagaacttatccaaaactttc--tgctgcgttttgc--gctgcttatactgg-agtgtt----ttttttcattattggcagAAAAGTATGAGCCGGTCAACGTGAAATGGACAACCGAGCGATGTGCAGTTTGCAGATGGGTGGAAGATTGGGACTACAACAAGATCATTATCTGCAACAG
||| | || ||||| ||||| || || | | || || | | | | | | || | || | ||| ||| || | || ||||| ||||| | || || || ||||||||||| || |||||||||| || |||||||| ||||| ||||| |||||||| || | ||||| |||||
gtaactcaacttcaatttagatcttccaagttgcctgtagtattgaatgatccttctcacaagggaattggattgatggagttaaaatttatttacattttacagAACCATATGATACTGTAAATGTAAAATGGACAACAGAAAGATGTGCAGTCTGTAGATGGGTTGAAGACTGGGATTACAACAAAATTGTAATCTGTAACAG
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 10
gtattaagc---aattcggatctcag-aactta----tccaaaactttctgctgcgttttgcgctgcttatactggagtgttttttttcattattggcagAAAAGTATGAGCCGGTCAACGTGAAATGGACAACCGAGCGATGTGCAGTTTGCAGATGGGTGGAAGATTGGGACTACAACAAGATCATTATCTGCAACAG
|||| |||| ||| |||| || | |||| | || | || || | | || | ||||| | ||| | ||||| ||||| || || || || |||||||| || || |||||||||| || |||||||| ||||||||||| |||||||| || | || || || ||
gtataaagctttcattttaatcttagtagcttagttgttttgaagatacttctcccagcagatttgaattcg-tggagcttgaatttgtttcccatgcagACCCATATGATCCTGTAAATGTAAAATGGACGACAGAAAGATGTGCAGTCTGTAGATGGGTTGAAGATTGGGATTACAACAAAATTGTGATTTGTAATAG
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 11
---gtattaagcaattcggatctcaga-acttatccaaaactttctgctgcgttt------tgcgctgcttatactgg-agtgttttttttcattatt-----ggcagAAAAGTATGAGCCGGTCAACGTGAAATGGACAACCGAGCGATGTGCAGTTTGCAGATGGGTGGAAGATTGGGACTACAACAAGATCATTATCTGCAACAG
|| | |||| | | || | | | | || || || || |||| || | || ||| || | | || | | | |||| | |||| |||||||| || || | | || ||||| || || || ||||| ||||| |||||||| ||||| |||||||||||||| || || || ||||||||
gtgacttttacttattctgtttgcatacaacttttca-----ttttgatgagttttccaaatgaagttctcatagtgataattttactgtaaactatttctctgacagAGAAGTATGAACCTGTTCATGCTAAGTGGACTACAGAACGCTGTGCTGTTTGTAGATGGGTTGAAGACTGGGACTACAACAAAATTATCATTTGCAACAG
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 11
---gtattaagcaattcggatctcag--aactt---atccaaaactttctgctgcgttttgcgctgcttatactgga-gtgttttttttcattat--tggcagAAAAGTATGAGCCGGTCAACGTGAAATGGACAACCGAGCGATGTGCAGTTTGCAGATGGGTGGAAGATTGGGACTACAACAAGATCATTATCTGCAACAG
|| | |||| | | ||| ||||| || | | ||| | | || | | | | || | | ||| || |||| |||||||| || || | | || ||||| || || || ||||| ||||| |||||||| ||||| |||||||||||||| || || || ||||||||
gtgacttttactcattctgtttgcagacaacttttcattttgatgagtttgccatatgaagttctcttagtgatagttgtactgtaaactatttctctgacagAGAAGTATGAACCTGTTCATGCTAAGTGGACTACAGAACGCTGTGCTGTTTGTAGATGGGTTGAAGACTGGGACTACAACAAAATTATCATTTGCAACAG
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 2
----gtattaagcaattcggatctcaga--acttatcca------aaactttctgctgcgttttgcgctgcttatactggagtgttttttttcattattggcagAAAAGTATGAGCCGGTCAACGTGAAATGGACAACCGAGCGATGTGCAGTTTGCAGATGGGTGGAAGATTGGGACTACAACAAGATCATTATCTGCAACAG
| |||| ||| || | | |||| | | || ||| | || |||| | || | | || |||| || |||| |||||||| || || | || ||||| || || |||||||| || || |||||||| ||||||||||| |||||||| || || || ||||||||
gtaccttttaactccttcctattttgtatgactttacaatgtgataagtttttagatgaattttttagagtgacaacggtactgcaattttct----ctgacagAGAAGTATGAACCAGTTTGTGCTAAGTGGACTACAGAACGATGTGCTGTATGTAGATGGGTTGAAGATTGGGATTACAACAAAATTATCATTTGCAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctgctgcgttttgcgctgcttatactggagtgttttttttcattattggcagAAAAGTATGAGCCGGTCAACGTGAAATGGACAACCGAGCGATGTGCAGTTTGCAGATGGGTGGAAGATTGGGACTACAACAAGATCATTATCTGCAACAG
ttttttttcattatt CT-rich tract
tgttttttttcattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaagcaattcggatctcagaacttatccaaaactttctgctgcgttttgcgctgcttatactggagtgttttttttcattattggcagAAAAGTATGAGCCGGTCAACGTGAAATGGACAACCGAGCGATGTGCAGTTTGCAGATGGGTGGAAGATTGGGACTACAACAAGATCATTATCTGCAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA