Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttatcacacggagcttgcgtttctgagttaaatgaatgtacctaaacaaatgcttcgttgcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30920.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G178958_T01 (Zea mays), 3'ss of exon 5
-----------------gtaagtttatcacacggagcttgcgtttctgagttaaatgaatgtacctaaacaa-----atgcttcgttgcacaat---cagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
| | | || | | | || | | | || | | || || || ||| || || | | ||||| |||||||| ||||| || ||||| |||||||| ||||| || || ||||||||||| || | | || || || || || ||||| ||||||
gtacttcatttttcacagccgcctagctgtatagatgtagaggtttt-acccatattagtttatctgttaaatttctatgtttttttccccttctcacagGTTCACTTTATAGTCGCTGCCTGTGAAAATATGATCAGTGGCACAGGCATGAGACCTGGTGACATTGTAACTGCTTCCAATGGGAAGACAATTGAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G028114_T01 (Zea mays), 3'ss of exon 9
-----------------gtaagtttatcacacggagcttgcgtttctgagttaaatgaatgtacct---aaacaaatgcttcgttgcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
| | | || | | | || | | |||| | | || || || ||| || | ||||| |||||||| ||||| || ||||| |||||||| ||||| || || ||||||||||| || | | || || || || || ||||| ||||||
gtacttcatttttcacagccgcctagctgtatagatgtagaggtttt-acccaaattagtttatctgttaattctatgtttttcccttctcacagGTTCACTTTATAGTCGCTGCCTGTGAAAATATGATCAGTGGCACAGGCATGAGACCTGGTGACATTGTAACTGCTTCCAATGGGAAGACAATTGAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G08150.1 (Glycine max), 3'ss of exon 5
----------------------gtaagtttatcacacggagcttgcgtttctgagttaa--atgaatgta---cctaaacaaatgcttcgttgcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
|| || | | ||| | | | | | ||| ||| | || | | || | | | || ||||| || |||||||| |||||||||||||||||||||||||| || || ||||| ||||||||| | ||||||| ||||| |||||||| || |||
gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtagtaatgataatgcatgcaatgcccagattaaaaatcc--tacatgtgcagGTTCATTTTATTGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 5
--------------gtaagtttat-cacacggagcttgcgtt----tctgagttaaatgaatgtacctaa-acaaatgctt-----cgttgcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
|| | || | | | | | ||| | | | || |||| | || | | | || | |||| ||||| || ||||| || |||||||||||||||||||||||||| || || ||||| ||||||||| | ||||||| ||||| |||||||| || |||
gcatatgttgttgaataggattgtgcttatagcttctttgttcatctttttgcacaaaaaatgcatcttatatcccagtttaaaaaccctgcatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 5
---------gtaagttta----tcacacggagcttgcgt------ttctgagttaa-----atgaatg---tacctaaacaaatgcttcgttgcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
| ||||| || | ||| ||| || || || | ||| ||| ||| |||| | | || | | | || ||||| || ||||| || |||||||||||||||||||||||||| || || ||||| ||||||||| | ||||||| ||||| |||||||| || |||
tggtggctaatttgtttagagttctgatggatattgtgtagtatcttttgtggtaataataatgcatgcaatacccagattaaaaatcc--tacatgtgcagGTTCATTTTATAGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGTATGAGGCCTGGAGATATTGTCACAGCTTCAAATGGAAAGACTATAGAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 5
----gtaagttta----tcacacggagcttgcgt------ttctgagttaaatgaatg-tacctaaacaaatgcttcgttgcacaatc----------agGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
| ||||| || | |||| ||| || || || | | || |||| || | ||||| | | | |||| |||| || |||||||| ||| | |||||||||||||||||||| || | ||||| ||||||||| | ||||| | ||||| |||||||| || |||
gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
upper sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------------gtaagtttatcacacggagcttgcgtttctgagttaaatgaatgtacc-taaacaaatgcttcgtt---------gcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
| ||| | | || | |||| || ||||| || | || || ||| | || | | |||||||| || ||||| |||||||||||||||||||||||||| || || ||||| |||||||| || ||||||| ||||| |||||||| ||||||
gtaagccagttgttgttgttgttgttatcattgtttgtttgttttaacttgcatggaacaatttcttaactaatccatttgt-atgttctattttcaattctccagcaattgaatctagcatacacttatgacttattaagggtcttgtatttgcagGTGCATTTCATTGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGCATGAGGCCTGGAGACGTTGTCACAGCTTCAAATGGAAAGACAATTGAGMapped 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|125083386|gb|EL143964.1|EL143964EST: AGCCATTGGTCAAATTAAGCCTCCAGGTGTTTGAG GTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAAT
genomic: AGCCATTGGTCAAATTAAGCCTCCAGGTG-TTGAGgtaagtttat ... gcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcgtttctgagttaaatgaatgtacctaaacaaatgcttcgttgcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
acctaaa putative branch site (score: 3)
ttaaatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttatcacacggagcttgcgtttctgagttaaatgaatgtacctaaacaaatgcttcgttgcacaatcagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG