Sequence
atgc intronic sequence ATGC exonic sequencegtattgttgacttaattagattcttaatctagctcttttcatgtgctttagaggattcttgatcatgtagctcttttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56500.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 5
------------------------------------------------------------------------------gtattgtt-gacttaattagattct-taatctagctct-tttcatgtgctttagaggattcttgatcatgtagctcttttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
| | | | |||| | | | || | || || || | | || |||||| |||| | || | | ||| | |||||||||||||||| || || |||||||| ||||| ||||| || |||||||| ||| | || |||||||| ||||| || ||| || ||||| | |
gtaaaataatcgtcaggctctaatgctttcagaatgttttagttgtggttgtggcaacctggtgtttgttgcaacaatgcttagctagactgagtcaaatcagatgatttatctatgtagtatatgcttttttttgttct-acttataaaaaacattttcttgctttagGTTGAAGACAGTGAGCTTGCGGATGTTGCTGCAGTCAGTGCTGGCAACAATTATGAAATCGGTAATATGATAGCAGAGGCTATGAGCAAGGTTGGCAGGA
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 5
-------gtattgttgact--taattagattcttaatc--tagctcttttcatgtgctttagaggattcttgatc-atgtagctcttttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
| | ||| || | || || || || || ||| | | || | | | | ||| || | | | ||||||||||||||||| ||||| || |||||||| || || ||||| ||||| || |||||| | ||||| ||||| || ||||| ||| || ||||| ||
gaattcaggagcattggctgccagtttgaatcgtactcatccgctacagcactatttttgcttgaaatttgaatctatcatattgcatgcaactttgcagGTTGAAGACAGCGAACTTGCTGATGTTGCTGCGGTAAGTGCTGGAAATAACTACGAAATTGGCAACATGATAGCTGAAGCTATGAACAAGGTTGGACGAC
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 5
gtattgttgactta-attagattcttaatc----tagctcttt------tcatgtgctttagaggattcttgatcatgtagctctt---ttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
|| |||| | || || ||||| || | || || || || | | ||| |||| |||| | || || ||| |||||||| |||||||| || || |||||||| ||||||||||| ||||| || || ||| | || |||||||| || || || ||| ||| ||||| ||
-gataattgattcccgtttgaatcttattcatttcaacttttaagaatactattccctcttcaaaatt-ttgaatatgttggactaacatttgatattacagGTTGAGGACAGTGAGCTTGCTGATGTTGCTGCAGTTAGTGCGGGAAATAACTATGAAATTGGGAATATGATAGCTGAGGCTATGAAAAAGGTTGGGCGGC
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------------------------gtattgttgacttaattagattcttaa--tctagct-cttttcatgtgctttagaggattcttgatcatgtagctcttttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
|| | || | | || ||| | || | ||||| | | ||| | || |||||| | || || |||||||||||||||||| ||||| | |||||||| |||||||| |||||||| |||||||| |||||||| ||||||||||| |||||| || | ||||||| | |
gtgaagcatttttctattattgttgaaataccaaacattgttgtgtgtctgtgtgtaagcgtgtttattgtatggtgtactcaaattttcccattttttaatatgtttagtgtttaattatttttcttatctttttgttgagacttgataaggttctggttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCAGGGAACAATTATGAAGTAGGAAATATGATTGCTGAAGCATTGAGCAGAGTTGGTAGAA
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------------------------gtattgttgacttaattagattct-------taatctagctcttttcatgtgctttagaggattcttgatcatgtagctcttttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
||| || | || || | || |||| | ||| | | | ||| | || |||||| |||| | || |||||||||||||||||| ||||| | |||||||| |||||||| ||||| || |||||||| ||||| || |||||||| || |||||| || | ||||||| | |
gtgaagcatttttctacttattgttgaaataccaaacattgttgtgtgtctataagcatgattattacatggggtactaaaaatttcccaatttttaatatattttagtgctccgttactaattcattaatttgcttatctttttgttgagacttgat-atgtgg---ttgggtggattgcagGTTGAAGATAGTGAGTTGGCAGATGTGGCAGCAGTCAGTGCTGGGAACAATTATGAAGTGGGAAATATGATAGCTGAAGCATTGAGCAGAGTTGGTAGAA
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------------------------gtattgttgacttaattagattcttaatct----agctcttttcatgtgctttagaggattcttgatcatgtagctcttttctgg-attgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
|| | | | ||||| | ||| ||| | || || ||| | | | || || | | | | | ||| || ||||||||||||||||| ||||||||||||||||| ||||||||||||||||| | ||||| || ||||||||||| ||||||||| ||||| ||||| |
gtaattgagaaatactatttcaaggtcttgcgttgattgagaattatgtctctagtctagtcttaagttcatttgaaattttaaaagttcatttttacttttatctagaatgtctaggatctaaacagtaatatggtatcacagGTTGAAGACAGTGAGCTAGCAGATGTTGCAGCTGTTAGTGCAGGAAACAACCATGAAGTGGGAAATATGATTGCCGAAGCAATGAGTAAAGTGGGTCGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttttcatgtgctttagaggattcttgatcatgtagctcttttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
tcttgat putative branch site (score: 4)
ctcttttct putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgttgacttaattagattcttaatctagctcttttcatgtgctttagaggattcttgatcatgtagctcttttctggattgcagGTTGAAGACAGTGAACTAGCAGATGTTGCAGCAGTTAGTGCAGGAAACAATTACGAAGTAGGCAATATGATTGCAGAAGCAATGGCAAAAGTTGGTCGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA