Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08040.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 7
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtca---tgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
|||| | | | || | | | ||| || | | || | ||| | || ||||| | ||| | | | | || | ||||||||||| || ||||| ||||||||||| |||| ||||||||||||| ||||| || |||||||| || ||||| || ||||| |||||||| ||
-------gtctgctactttgctctg-atgctattgtc-attctctcaggtgctcaattttgaaggatatcttctaaagatttatttatgcacatacat-----gtagGTGGTATGCCAAAAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATCTGGGATGAGGACCTTGGGGTGGAGCATTTCAATGCGGAG
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttat-ctacaaaatcctcaccttg-----agctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
||| | || | | || | | | ||| || | | || | | ||| ||||| | || || || | | || | |||| | | ||||||||||||||| | |||||||||||||||||||| | ||||| || ||||| || |||||||| || || || || ||||| |||||||||||
gtaggtaa----aggttattgttattatta-atatgttatctgtgctga-atccatttgaatttttgctgtgaagtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 7
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctc---accttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
|| | | | || | || | ||| | | ||||| | || || | || |||||| || | ||||||||||| || ||||| || || |||||| | || || |||||||||| |||||||| ||||| || ||||||||||| ||||| || || |||||
--------------------gtacactctgc-tcctttgatatcctttataattgtctaaattgga--aggtgattctaaagatactgttttgtttaaatt--gtagGTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAG
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 6
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaat--agtcatgaaaatttatctacaaaatcctca---ccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
|||| || || || || | | | | || |||||| | || | |||| | || ||| || | || || ||| | | | ||||||||||| ||||||||||| ||||||||| |||| | | ||||| || |||||||| |||||||| ||||| | || | || |||||||||||
gtaaattattgtaa---cagatcc-tgttgtgttttttcat-cttctagtttagcactatgtatttgacaaccaaaggctaagtgttttactctttttttttatacaagGTGGTATGCCAAGAGATTTTTACATCCTGATATTGTTGCCCCGTATGACTACATATTTATCTGGGATGAGGATCTAAGTGTACAACATTTCAATGCAGAG
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
| | | | ||| || | | | | | | || | || | | | || | | ||| || | || | ||||||||||| |||||||| ||||||||||| |||| ||||||||||||| ||||| || |||||||| || ||||| || || || || ||||||||
---gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtttgtgc-acacaactct---agGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G801369_T02 (Zea mays), 3'ss of exon 7
-gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatcta-caaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
||| ||| | || | | || | | | || | | ||| | ||| || | |||| || | | | | | | ||||||||||| || ||||| | |||||||| |||| | || || || |||||||| ||||||||||||||||| ||||| || || ||||||||
cctaaacaattccta-tg-aattttctgcgttccaaaggggcccctc-agtctctatgca--tttgtccatcaaaggttgcaaacttattt-ctcgtttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTACATATTTATCTGGGATGAAGATCTTGGTGTCGAACATTTTAATGCAGAG
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G119725_T04 (Zea mays), 3'ss of exon 7
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
||| | | |||| | || || | | | ||| || | || | ||| || ||| | | ||| | | | | | |||||||||||||| ||||||||||||| |||||||| | ||||| || || || || |||||||| ||||| || || ||||| ||||| |||||
gtatggtagtattgctgtaatt--atacaatgtctttttattgcccttgtcaatataatgttttgacttcaattttattgatgtgattcttgtgtttatacaagGTGGTATGCAAAACGATTTTTGCATCCCGATGTTGTTGCCAGATATGATTACATTTTCATCTGGGATGAGGATCTAGGTGTAGAGCATTTCAACGCAGAG
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------------------gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgttt-----------atctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
|| | | | || | | | | | | || || | || ||| |||| | | ||| | | || | ||| || || ||||||||||||| || ||||||||||| |||||| | || ||||||||||| ||||| ||||| |||||||||||||||||||| || ||||||||||||||
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaatt-cttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------------------gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
|| | | | || | | | | | | || || | || ||| |||| | | || | | ||| | || | || || ||||||||||||| || ||||||||||| |||||| | || ||||||||||| ||||| ||||| |||||||||||||||||||| || ||||||||||||||
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctattttttggtgatcacatttaactttggaatt-cttaaaagaccttatcattcttaggagtgatgaccttattgcttttatgcaatttcctcgtact--taatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
| | | | | | | | || | || | || |||| || | | || | || | | | | | || | || | | |||||||||||||||| || || ||||||||||||||||| | |||||||| ||||| ||||||||||||||||| || | || |||||||||||| |||
ggagagacacggcattattggctaagctgaaa----ctttttctgctgcagatagttaatactttttgtcctagtttatattcatagattcccatgtattgcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG
upper sequence: AT1G08040.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
gtaagaaatctgaaatgtaggtcagcacgatatac--tctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
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-----atgcctgtttgttacttgtggtggattctcaatctgactacatttctggctctgctctgttgtcgaagttgtagttaact-gattttaggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGGMapped 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|164068536|gb|ES202751.1|ES202751EST: GAGTGGTCTAAAAATGCAATACATATCAGTGCAAAAAAGCAAACAAAATG GTGGTATGCAAAGAGATTTT
genomic: GAGTGGTCTAAAAATGCAATACATATCAGTGCAAAAAAGCAAACAAAATGgtaagaaatc ... tctttggcagGTGGTATGCAAAGAGATTTT
EST:
gi|164062711|gb|ES203794.1|ES203794EST: AGTGGTCTAAAAATGCAATACATATCAGTGCAAAAAAGACAAACAAAATG GTGGTATGCAAAGAGATTTT
genomic: AGTGGTCTAAAAATGCAATACATATCAGTGCAAAAAAG-CAAACAAAATGgtaagaaatc ... tctttggcagGTGGTATGCAAAGAGATTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
tcctcac putative branch site (score: 2)
tttatcttt putative PPT
atgaaaatttatctac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaatctgaaatgtaggtcagcacgatatactctaattcttctaatagtcatgaaaatttatctacaaaatcctcaccttgagctgtttatctttggcagGTGGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT