Sequence
atgc intronic sequence ATGC exonic sequencegtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G29040.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 4
-gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG-
|| | | | | || || | | ||||| | || || | | | | | || || | |||| | | ||||| |||||||||||| |||| |||||||| |||||||||||||| |||||||||||||| ||||| || || || || || ||||||| | | | | |||
tttataatgtgctcgctcattgattatgtctggaagaaaca-atttgcatggtcctc-------acttccacattcttaccgtggtgtgctgttttatgattt-cacagGTGACACATGCTGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAGGAAGGTGTGCCGGAGGGTCTTTACATGTGATGTGCTCACTG-GTCGC
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------------------------gtagagactcttaaccattt-agttcaagc-acatacaaacacacacacacacaccacttgggcaattacta-gccactgacgcta-atgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG-
|| | ||| || | |||| ||| | || | ||| | || | | || | | || || || || | || || || ||||||||||| | ||||||||||| || || |||||||| |||||||||||||| ||||| || || ||||| || || |||| | | | || ||
gtaactcagctttgttttctcaaccagactccttgctctctagtactgttaatgttaaaactttcgagcatactaagtgccaatcctttcagatctgagtttgagctgcgctcaga-acatatttgcatggaatgcaagtctttgttgcacttctctttttacatttgctgttcttctgttgctttagGTGACACATGCCGATTTCAAGAAGGCCAAAGAGAAGGTCATGTTCAAGAAGAAGGAAGGTGTACCGGAAGGGCTTTATATGTGAGACATCCACCAC-TCAT
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 4
----gtagagactcttaacca-tttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG
| | | ||| ||| ||| || || | | | || | | || ||| | | | || || || |||| ||| |||||| |||||||| ||| | |||||||||||||||||||||||||| |||| ||||||||| ||||| || || || || ||||||||||| | || | |
ttttagtgtgtgtattacccaatttgctttaactatgtctgagcatata-----gtactttatggtt--ccatttgacattg---ctgatgt-tttgttttggat--acccagGTGACCCATGCAGATTTCAAGAAAGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGTAGACGTCTCCTGCCT
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G095593_T02 (Zea mays), 3'ss of exon 1
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactga----cgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTA---AAATTATA-ATCATATCG--------------------------------
| | | ||||| | | | ||| |||| ||| |||| ||| |||| | |||||||| ||| | ||||||||||| |||||||||||||| |||| ||||||||| ||||| || || || || ||||||||||| || ||| ||||| ||
-----------------------------------------------atatagcacttcgatc-tgattaggttctgagatttgctgatgtttttgttttgggtacacccaggtgacccatgcagatttcaagaaggcaaaggagaagGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGCCAATCTATTCATCATGCCGAACAAGTTACCCGATTGTGTGTGTACTAGCAC
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 4
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactga----cgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAA-ATTATAATCATATCG
| ||| || | || | | | | ||||| | | | ||| |||| ||| |||| ||| |||| | |||||||| ||| | ||||||||||| |||||||||||||| |||| ||||||||| ||||| || || || || ||||||||||| | | || ||||
---------tccatttgcatagcataactgtct-tgtctacttgga-atatagcacttcgatc-tgattaggttctgagatttgctgatgtttttgttttgggtacacccagGTGACCCATGCAGATTTCAAGAAGGCAAAGGAGAAGGTGATGTACAAGAAGAAGGAAGGTGTTCCGGATGGTCTCTACATGTAGCCAATCTATTCATCAT-
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAA-TTATAATCATATCG
| || | || | | | | | || || | ||| | || || | ||| || | | |||| || || | |||| || ||| | || |||||||| || || || ||||||||||||||||||||||||||||| || || ||||| || |||| | | | || | || |
------attcaccagagttaaccttttgtaatagcctgca-acttgaatacaaggtcacagaaaatatccactcatga-actgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTCATCAGCAGCGC-
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 5
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAA--ATTATAATCATATCG
|| || || |||| ||| || | | | || | | | | | | | | | || |||| | |||||||||| ||| | || |||||||| |||||||| ||||||||||| |||||||||||||| || || ||||| || || |||| || || | ||||| |
-aagtgatcct-----attttgttttc-tacctttttttggaggggtgtgtgtcttttcctttactctcatgaccaaatgttttttttttaaaatcttgctc-ttcagGTGACGCATGCCGACTTCAAGAAGGCAAAGGATAAGGTTATGTTTAAGAAGAAAGAAGGGGTGCCAGAAGGACTGTATATGTGAAGCATCTTCATCATTT--
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 5
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttg---ttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAA--ATTATAATCATATCG
|| | | | || || | ||| ||| | | || || | | |||| ||| || ||| |||||||||| ||| | || || ||||| |||||||| || |||||||| |||||||||||||| || || ||||| || || |||| || || | |||| |
----------tttatattcaattttctctgtattttattttgttt-tgcaccttttttgagtggtgtgtaccctcgtgaccaaatgcttttttttttatcttgctcttcagGTGACGCATGCCGACTTTAAGAAGGCAAAGGATAAAGTTATGTTTAAGAAGAAAGAAGGAGTGCCCGAAGGACTGTATATGTGAAGCATCTTCATCAATT--
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 5
gtagagactcttaaccatttagttcaagcacatac-aaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCA-TATCG
| || | | || | | || | | | | || | | | ||| | | | | |||||||||||||| ||| | || || ||||| || ||||| || || ||||| |||||||||||||| || |||||||| || || |||| |||| || | ||||
--------tgtttaatgtgtatctttggtttgtattgtatataatataatttgaagttttttttctccccaatttatgatatcttcttactattacttt-tttgttcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAATACTATCCTCTATC-
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG
|| || | | | |||| | | | ||| || || | | | ||| | | | || |||||| | |||||||||| ||| || |||||||| |||||||||||||| |||||||||||||||||||| || || ||||| || ||||||| ||| | | ||
--ggaagaagttgaatgcattacctgactacatgtttgctgattt-tagtcac--ctaggaccaggatc--ccaattaaatttgactggttaaatactgtgc-ttcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 5
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG-
| || | || || ||| || | ||| | || || | ||||| || || ||||||||||||| || || |||||||| |||| ||||||||||||||||||||| || ||||| |||||||||| | || | |
----------------------------------------------------gtagtttctcgat-gcttttcac-aactttcttgtaacgattttcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAA-TAGCCGTCCCAGCTT
upper sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 5
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG-
| || |||| || ||| || | ||| | || || | ||||| || || ||||||||||||| || || |||||||| |||| ||||||||||||||||||||| || ||||| |||||||||| | ||| | |
----------------------------------------------------gtagtttctcaat-gcttttcac-aactttcttgtaacgattttcttcttctccagGTAACTCAAGCTGATTTCAAGAAGGCGAAAGAGAAGGTCATGTACAAGAAGAAAGAAGGCGTCCCGGAGGGCCTGTACATGTAAA-TAGCCATCCCAGCTTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86082474|gb|DR378233.1|DR378233EST: CTATATGCACTGAGGCTGGTCTACTAGCTCTCAGGGAGCGTCGTATGAAG GTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAG
genomic: CTATATGCACTGAGGCTGGTCTACTAGCTCTCAGGGAGCGTCGTATGAAGgtagagactc ... atttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG
tttgttc CT-rich tract
taatgtgtttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagagactcttaaccatttagttcaagcacatacaaacacacacacacacaccacttgggcaattactagccactgacgctaatgtgtttaaattggatttgttcagGTGACACATCCTGATTTCAAGAAAGCAAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGCGTCCCTGAAGGCCTCTACATGTAAAATTATAATCATATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG