Sequence
atgc intronic sequence ATGC exonic sequencegtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G58140.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttga-tctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
| | ||| | | | | || | ||||| || ||||||| ||| | | ||| | | | | | | || ||||| | ||||| ||| |||||||||| ||||| |||||||| || || || || ||||| || |||||||||||| ||
--------------------------------------------------------------------gtaaactagttatagttagttctgtctttgtcaccaaagaaatttatcaaatatatatgcattggtttaaatataaagaaacatgtgtg-----cagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG
upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 4
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
|||||| | || | | || || | ||| | ||| | ||| || | | | ||| || || ||| | ||||| ||||| | || |||||| |||||||||| ||||| |||||||||||||| ||||| |||||||| || ||||||||| ||
------------------------------------------gtaaatcattt-----gtagcttgttccttatcatttgaggggatgacgaaattgatccttgtt----tcagataaac---tatagaaaaatgtcatctg-------------------cagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG
upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 4
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
| | || | | | | ||| ||| || || | || | || | || | | | || | | |||| |||| | || |||||| |||||||||| || || |||||||||||||| ||||| |||||||| || ||||| ||| ||
--------------------------------------------------------------------gtaaatcacttgtaacttgtttcttgtta-tttgaggggatgatgaaatag-atccttgtttcagctaaactatagaaaaatggcat--ctgc-agGTGCTGTAGAGATGCGATGGGTTGACACTTACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATACTTTCAG
upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 6
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG-----------------------
| | || || ||| ||| | || |||| || ||||| || | | | | |||| | || ||||| | ||||| | ||||| ||| | ||||| ||||| |||||||||||||| |||||||| ||||| ||||| |||||||| |||
------------------------------------------------agcctcctccatctccctctaaccaaacattatgtaaatgattttctttttttaaatagccttc-------tctgcgc------attta---tagtttttcccttttgcgtttcagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCGTTTGAACTTGAAATATATTTCAAGGCATGCTATGCATACTTATCTCT
upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 4
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
| ||| | | ||| || | |||| | | || | || | || ||| | || | | ||||| ||||| || | ||||| | ||||| ||| | ||||| ||||| |||||||||||||| |||||||| ||||| ||||| || ||||| |||
------------------------------------------------tatacacaaggcgtctagttatgaactt------gtgatattcctttgaagtcaaatataatttgcaaagctacgtacttataaattt--------tcccttttactgttt--cagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG
upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 4
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttgg--ctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG------------
|| | | | | | || | | | ||| | | || | | |||||| | | ||| || | || ||| | | ||| | ||||| ||||| ||| | ||| |||||||||||||||| || ||||| ||||| ||||| ||||||||||||||| ||
--------------------------------------------------------tcttgaaatttctgaaatctatcagaaaggtagttt--tcatcttggggtttacc-------atatactgtatagaatctg-tgtgggctaaatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA
upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 4
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttgg--ctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
|| | | | | | || | | | ||| | | || | | |||||| | | ||| || || ||| | | ||| | ||||| || || ||| ||| |||||||||||||||| || ||||| ||||| ||||| ||||||||||||| | ||
--------------------------------------------------------tcttgaaatttctgaaatctatcagaaaggtagttt--tcatcttggggtttacc-------atatactgtatagaatctg-cgtgggctaaatctgttgaaatttgcagGTAATGTAGAAATGCACTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTGTCAG
upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 5
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
| | | || ||| | || | | ||| || |||| | || | |||| || | | ||| | | || ||| | || | || ||||| ||||| ||| | ||| |||||||||||||||| || ||||| ||||| ||||| |||||||| |||||| ||
-----------------------------------------tcttga-aatttctgaaatctatcagaaag-gtggttt-------tcatcttgg-ggtttaccaaatactgtatagaatctgcgtgggctaaatctattgaaatttg-------------cagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATGTATTTTCAG
upper sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 4
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaata-tacatgaaataatt-tgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
| | ||| || | | | | | | || | |||| || || ||| | ||| | ||| ||| || || | | || | ||||| ||||| ||| | ||| |||||||||||||||| || ||||| ||||| ||||| ||||||||||||||| ||
--------------------------------------------------ccttaaaa-----tttctgaaatctatcagaaaggaggttgtcatc---ttgag-----gtttaccatatactgtatggaatctccgtgggctaaatctgtt---gaaatttgcagGTGATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGMapped 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|116411244|gb|EG453836.1|EG453836EST: TGCTGAGGATTTGAAGAAATGTCTTGAGGGATTGGCACGCCACTTATTTG GTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCAT
genomic: TGCTGAGGATTTGAAGAAATGTCTTGAGGGATTGGCACGCCACTTATTTGgtacattaag ... tggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCAT
EST:
gi|116422564|gb|EG465156.1|EG465156EST: TGCTGAGGATTTGAAGAAATGTCTTGAGGGATTGGCACGCCACTTATTTG GTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCAT
genomic: TGCTGAGGATTTGAAGAAATGTCTTGAGGGATTGGCACGCCACTTATTTGgtacattaag ... tggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
atttgat putative branch site (score: 5)
cttctttttttggct putative PPT
aaatatacatgaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttggctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT