Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
|| || | || || ||| || | |||| || | ||| | | |||| || ||| | || || | | | || | || | || | || | |||| ||| |||| ||||| |||||||| || | | ||| || | |||||||||||||| || ||||||||||| |||||||||||||| |||||
gtttgct-tgcttctcatcttct---tttcatgataacc------gccttg--cgtttatcatagtatttcctaatat--tcctattatgttctgatat----gacttgtttc-cat----agGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 8
gtatgttgtgaatccaatcctccggctctcattatgtcttgcag-ggccgtaatccct-tataatggtacgttctgatttcgtgcaatga-cgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
|||| ||| || | | |||| | | | | | | | || || || | | | | | | |||| | || ||||| |||||||||||||| | || | |||| | ||||||||||||||||| ||||||||||| ||||| || || ||||||||
--------------------------tctctttagaatatggattaaatgaaatctttctgtgactaaaagaaaataatttgtctgatcctcttcatgtgatactataaatttgtgttgcttgcagGTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 11
gtatgttgtgaatccaatcctccggctctcattatgtcttgcag-ggccgtaatccct-tataatggtacgttctgatttcgtgcaatga-cgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
|||| ||| || | | |||| | | | | | | | || || | || | | | | | | |||| | || ||||| |||||||||||||| | || | |||| | ||||||||||||||||| ||||||||||| ||||| || || ||||||||
--------------------------tctctttagaatatggattaaatgaaatctttctgtgactaaaagaaaataatttgtccgatcctcttcatgtgatactataaatttgtgttgcttgcagGTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
| | | ||| | ||| | | | | |||| | | ||| | || || ||| | | || | | | | | | || ||||| |||||||||||||| | || | |||||| | |||||||| |||||||| |||||||||||||||||||||||||| ||||
-------------------acgcaaccatacatatat-ttgtaaattct---ttctttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataat--ggtacgttctgatttcgtgca-atgacgtagtaatttcttcaacatttttcac---atttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
|| ||| ||| | | | || | || |||| | || | | | |||| | | || | |||| || | || | ||||| || ||||||||| | || ||||| | ||| | ||||||||||||||||| ||||| |||||||| || |||||||| |||||
-----------------------------caacatgctttgtaagctgctcttcaatgttagccaggtatctagtgttgttaggtgcatgatattctcggttatctaacagttcataattaatctgcagGTGTGCGGGTTTGATTTACTCCGATCACAAGGCCGGTCATATGTTTGTGATGTTAATGGGTGGAGTTTCGTTAAGAACTCTTACAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------------------------------------------gtatgttgtgaatccaatcctccggctctcattatgt-cttgcagggccgtaatcccttata-atggtacgtt--ctgatttcgtgcaatga--cgtagtaatttcttcaacatttttcac--atttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
| | ||| || | |||| | | || | | ||||| | | | || || | | || | | | | | || | | || ||| | | | | ||||| ||||| |||||| | || ||||| | ||| | |||||||| ||||| || ||||| ||||||||||| |||||||| |||||
gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacgtgcgtaagacttctgacatactaggattacttacctgctccggtacttcgaaatgcttctgacaaaagggataattggcctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ07403 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaa-tgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
||| |||| || || | | | ||| || ||| | || ||| |||| || ||| ||||| ||||| || | |||||| | || | || |||||||| ||||||||||||||||||||||| || ||||| |||||
----------------------------------------------------------gtaa--gtacatt-tggtaacttccaagtggaagagttctcattttaacggttttggca------gGTGTGTGGTTTTGACCTCTTGCGATCTCAAGGGAGGTCTTATGTTTGCGATGTCAATGGATGGAGTTTTGTAAAAAACTCGTACAA
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ19878 (Selaginella moellendorffii), 3'ss of exon 10
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaa-tgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
||| |||| || || | | | ||| || ||| | || ||| ||| | ||||| ||||| ||||| || | |||||| | || | || |||||||| ||||||||||||||||||||||| || ||||| |||||
----------------------------------------------------------gtaa--gtacatt-tggtaacttccaagtggaagagttctcattttaacgttt-------tggcagGTGTGTGGTTTTGACCTCTTGCGATCTCAAGGGAGGTCTTATGTTTGCGATGTCAATGGATGGAGTTTTGTAAAAAACTCGTACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
ttctgat putative branch site (score: 3)
tttttcacatttcc putative PPT
tagtaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC