Sequence
atgc intronic sequence ATGC exonic sequencegtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgttgtttatcctgcatccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
Basic information
| species | Arabidopsis thaliana |
| transcript | AT1G01510.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 2
gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctct-tgtttcatcatcttcttctgttgtttatcctgcatccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
| || | || || ||| | | | | || || || | || | | ||||||| | | || ||| | | || |||| | ||| ||||||||||| |||||||| ||||| |||||||| |||||||| ||||| |||||||| ||||| ||||| || ||| | || ||||| |
---------ttttctgcattg-cta----tggtggtgccacttgttcatcatccatcttataaaaaaagaacttgttgttcagcaaa-atgatggatactatttatttgacatagGTAAGGGAGATGCCAAATGTTTTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATCACGATATTGCAGT
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g38900.1 (Oryza sativa), 3'ss of exon 3
gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgttgtttatcctgcatccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
|| |||| || ||| | | | || || || ||| | || ||| ||| || || | | | | | | | |||||| || ||||| ||||| |||||||| ||||| ||||||||||||||||| ||||| ||||| || || || || ||||| || | || ||||| |
-gatactcttctattttcttgatgtattctgtcgttca-gcatgatgattaaactagagaatgatcaa----tgtcattgattatacttttactgc--------tcactcacagGTGCGTGAGATGCCGAATGTATTAATTCTTCCTCGAAGTGCAGATTACAGTGAAGAAGTGTGGATTGAAATCAGAGAAAAGGCACTCGCAATATTGCAAT
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G418294_T01 (Zea mays), 3'ss of exon 3
gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctg--ttgtttatcctgcatccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
||| || | | ||| || | | || | || | | || | || | || | |||| | || || || |||||| || ||||||||||| |||||||| ||||| |||||||| |||||||| ||||| ||||||||||| || ||||| || ||| | || ||||| |
----------actttgcacttgtgatgcttg----ctgtacttata-atacgctaatagaaaagtcatgtttcaaacaaatgatttaatacttgttatgtgtt-cattgatcacagGTGCGTGAGATGCCAAATGTATTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAGATCAGAGAGAAAGCAATCGCAATATTGCAGT
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctg---ttgtttatcctgcatcca--ttatatcttgttttcattg----cagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
| ||| | || | | ||| | || | | | || | ||||| |||||| || | || | | | || | | | | || | | ||| |||||| ||| ||||||||||| |||||||| || || |||||||| |||||||| ||||| |||||||| ||||| ||||| || || |||| || || |
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaatt-caagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G476107_T02 (Zea mays), 3'ss of exon 4
gtatgactttcttttccagtgactaaacttcacatttgcgcctgcct--attctcttgtttcatcatcttcttctgttgtttatcctgcatccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
| | | ||| | |||| | | | | || || |||| || |||| | ||| | | ||| | | | |||||| ||| ||||||||||| |||||||| || || |||||||| ||||| || ||||| |||||||| ||||| ||||| || || |||| || || |
------------gtcctcgcagataaggacacgagttgctgttattttaacaccgttattgtttcattacattttgttcagcaaactgg--tgactgatcattgctgtg--tacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGCGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G394945_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------------------gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctg---ttgtttatcctgcatcca--ttatatcttgttttcattg----cagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
| ||| | || | | | ||| | || | | | || | ||||| |||||| || | || | | | || | | | | || | | ||| |||||| ||| ||||||||||| |||||||| || || |||||||| |||||| | ||||| |||||||| ||||| ||||| || || |||| || || |
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaatt-caagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 3
gtatgactttcttttccagtgac-taaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgttgtttatcctg-catccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
| | | | || | | | ||| || ||| | | | | || | || | | | |||| || ||| | || | | | || | | | ||||||||||| ||||| || ||||| || || ||||| ||||||||||||||||| || || |||||||| ||||||||||| ||||| ||||| |||||
------------ctcataatcatatatatattagatt-acgtctgtcagtctacaacaatgatagttttaatagatagattatactaacatactttgtgtgt-gtctgcgt--cagGTGAAGGAGATGCCTAACGTGTTGATACTTCCTCGAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATATTGCAAA
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgttgtttatcctg-catccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT-
| | | | | | || | | || | | | | || | || | | | | || || ||| | || | | ||| | ||| ||||||||||| ||||| || || || || || || | ||||||||||||||||| || || |||||||| ||||||||||| ||||| ||||| | ||
------------ccactcacaatcatatat-atatatatgtctatcagtctacaacaatgatagttttaatacatagatgatgctaacatactttgtg-catgtctgcat--caggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgt-tgtttatcctgcatccatta----tatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
| |||| | ||| | | || | | || | || | ||| | | | | | |||| ||| || || | ||||| || |||||||| ||||| || ||||| || |||||||||||||| ||||| ||||| |||||||||||||||||||| |||| | ||| || ||
----------------ggaaaaataaaatagccatacaca---atattttttatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccatcatgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatgactttcttttccagtg-actaa--acttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgttgtttatcctgcatccattatatcttgttttcattg-cagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
||| | | | ||| || |||| |||||| || | |||| | | | | || || | | || || || || || | | || || | ||||||| ||||||||| || ||||| ||||| ||||||||||| ||||||||||| ||||| ||| |||||| | || || ||||| | || |
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattaca--aatagaatggattcttcattaattatttgttcgacttctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT
upper sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatgactttcttttccagtgactaaa---cttcacatttgcgcctgcctattctcttgtttc--atcatcttcttctgttgtttatcctgcatccattatatcttgttttcat-tgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
||| | | | | ||| | | ||| |||| || || | |||| | | | | |||| || | | | || ||| | || || |||||| | | |||| | ||||||| ||| |||||||| || || ||||| ||||||||||| || ||||| |||||||| ||| |||||| || ||||| |||||| | || | |
gtacgtcgctatcttcaactttgcaaatcgcttcccacttcccactgcatggtgtttcatttctaatgaaatcaatgcgtcgttaa--ctaaat--gttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcatcttcttctgttgtttatcctgcatccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
tcttgttttc CT-rich tract
attatatcttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgttgtttatcctgcatccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
