Sequence
atgc intronic sequence ATGC exonic sequenceTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79990.5 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 17
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaa--attgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
||||| | |||||||||||||||||||| |||||||||||||| ||| | |||| || ||||| | ||||| || || || |||| ||| |||||| || | || ||| | | | | | ||| |||| || | | | | | | | | |||| ||| | |||||
TACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgctgacttttgatccaaaacaatgagtttcttttattttggtacctgtttctctttgaacctgttgatttggtttcttaataattttgttcct-----------------------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 16
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatg----agaatgtg------ctttccctcgcattatggt-tacagctggattatggt-gttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
||||| | |||||||||||||||||||| |||||||||||||| ||||||||||| || |||||| | ||| | || || || |||| || | ||||||| || | ||||| ||| | | | | | || |||| | | | || | || | | | | | ||| || | ||| |
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCAAAGGCACAATACAATAGgtttgttccaaaatgtaaactgatttttttctacgctcttttctctctctaatttatctttgcttttagatccgttttcta--tttcgtaacggc--agattat-----------------------------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G086015_T01 (Zea mays), 5'ss of exon 2
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgt-gctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || || || | ||| | || || || |||| ||| ||||||||| || || | | | ||| || | ||| | | || | | || ||| | |||| | | | | ||| | |||| | || || |
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgattatcggtttgtttcaaaatat------atattgactttttcttttctaa---tttatctctgcttttagacccatttt--ctattttgttgaagacaggtta-----------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 17
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || || || | ||| | || || ||||||| ||| ||||||||| || || | | || || || || || || || | | || ||| | |||| | | | | ||| | |||| || || | |
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCTAAGGCGCAATATAATAGgtttgtgattatcagtttgttc-caaaatatatat---tgactttt--tttttctaa---tttatctctgcttttagacccatttt--ctattttgtggaagacaggttat----------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G448913_T01 (Zea mays), 5'ss of exon 6
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || || || | ||| | || || || |||| ||| ||||||||| || || | | || || | || | | || | | || ||| | |||| | | | | ||| | |||| || || |
TACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCAAAGGCGCAATATAATAGgtttgtgattatcagtttgttccaa-----aatatatattgactttttcttttctaa---tttatctctgcttttagacccatttt--ctattttgtggaagacaggtta-----------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 18
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
|||| | ||||||||||||||||| || |||||||||||||| ||||||||||| || ||| | ||||| || || || ||||| || || || |||| | ||| | || | | | || | || | | | | |||| || | ||| || |||| || | |
TACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCAAAGGAACAACACAACAGgtgccatcctgtttgtctgttcaaaattttgtagtggttgt----taatttaaacttttatgtgccccaatgtttata-tgatttacttttggcttgcag---------------------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 17
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatgg--ttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
||||||||||||||||||| |||||||| ||||| |||||||| ||||||||| ||| |||||| | |||| ||||||||||| ||||| ||||| ||||| || | | | ||| || | || | || | |||| || |||| | | | | || | | |||| | |
TACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGCATCATAACAGgtagtagttattttctgttatgttgttacggaatgacccttactttctttatttagaaattatgttt-----gatatgttttgagaaaggcttttttgtaagggt------------------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 17
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
| |||||||| ||||||||||||||||| |||||||||||||| ||||||||| ||| |||||| | |||| ||||| || || ||||| ||||| ||||| || | ||| | ||| || | || | | ||| | || | | | || || ||| |||||| || |
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCCAAAGAGCATCATAACAGgta--ggacttaccttgttgcaagacaatgattg--attttctttcaatat--gtagaaatatgcttgatat-gtgtagaaattaaaaatgtttttggtaacagaat--------------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 17
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgt-gctttccctcgcatt--atggttacagctggattatggt--gttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
| |||||||| ||||||||||||||||| |||||||||||||| ||||||||| ||| ||||| | | || ||||| || || ||||| ||||| ||||| || || | || | | || | | | | | || | | || | || | | | || || ||| || |||
TGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCCAAAGAGCATCATAACAGgtagaagttagttaccttgtgttacgttgcaagataatgattaattttctttcaatatgttgaaatatgcttgatat-gtgtagaaattaaaaatgctttt-------------------------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 6
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagc-tggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
||||||||||||||||||| |||||||| || || ||||| || ||||||||| ||| |||||| | |||| ||||||||||| ||| | ||||| ||||| || | |||| | |||| ||||| || | | | | | || | || | | || | ||| |||| || |
TACTTTTAAGTTTGATTGAATACAAGACACTAGTCATGCGCGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCTAAAGAGTATCATAACAGgtagtagt---tattttcttttatgttat---tacagaatgacctttactttcattatttagaaattatgtttgatatgttttgagaaaggcttttttgtaaggga----------------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 17
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttcc-ctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
||||| | | |||||||||||||||||| ||||| ||||||||||| || ||| || | |||| | ||||||| |||||| | |||||| | |||||||| ||| | || || | || | | || | || || | ||| | ||| || ||| | || ||| | | || ||| |||
TACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCTCAAGAGCACTACAATAGgtactgaaattcatagtatactgacagcaaagtaattgtgtgaatttgatggt-gtagatgtgtcctca-ggttgtagtctgatttga--tagcttgctagatt------------------------------------------------------
upper sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 17
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
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TACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgta--aatttctactgttggctgttggtaaacaacagtaaaataagag-----gcaaacactta--caatgtagtatttggatcttcatgttttgtggggaattttgta------------------------------------------------Mapped 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|124896506|gb|EH972720.1|EH972720EST: GAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAG CGTGGCACACTTTTTGGAGTCACGTGGCA
genomic: GAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaat ... gttttgtcagCGTGGCACACTTTTTGGAGTCACGTGGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCTAAGGAGCACCATAATAGgtatgagaatgtgctttccctcgcattatggttacagctggattatggtgttagtaaacatgtatccaaggtcacataatggtttaaattgttttcctaaattcacgcattcctacttttctgattctcgacttcaaaatcctgttcgttttgtcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA