Sequence
atgc intronic sequence ATGC exonic sequence...cataaatctttaggctttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G77090.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os12g08830.2 (Oryza sativa), 3'ss of exon 1
--------cataaatctttaggctt-tggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
| | || ||| | | | | || | | | || | ||| | | || | || ||||| | || || || || ||||||||||||||||||||||||||| |||||||| ||||| || || ||||| ||||| ||||| || || || || ||| ||| |||| | | | |
tgcagtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaa-aggaactgctggattgttttcatgatatagtt----tgttcagACAGGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCT----
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os12g08830.1 (Oryza sativa), 3'ss of exon 1
----cataaatctttaggctt-tggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
| | || ||| | | | | || | | | || | ||| | | || | || ||||| | || || || || ||||||||||||||||||||||||||| |||||||| ||||| || || ||||| ||||| ||||| || || || || ||| ||| |||| | | | ||| |
gtagcttccattttttgtcatataaggatcatctttcaggcatgctatctgaaaaaa-aggaactgctggattgttttcatgatatagtt----tgttcagacagGTTGGAGAACATACCGTAGGCCAGACGACAAGTCCGGTGGACATGGAGTTGGATGGAGCCCAATCATTCCCTACAGCTTCAAAGTTCGTGATGGCTGGGA
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G087590_T05 (Zea mays), 3'ss of exon 1
cataaatctttaggctttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatg-taattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
| ||| | || || | || | | |||| | || | ||||| ||| | ||| | || | | | |||||||||||||||||| ||||| || |||||||| ||||| || || || || ||||| ||||| || || ||||| ||| ||| ||||| | | |
---------gtgagctcttcttcttctttttc----ttctttctctgcagtgaaatactgttgaatt-gttttcatgatgctgatcgaatcgttcagACAGGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCT----
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G087590_T01 (Zea mays), 3'ss of exon 1
cataaatctttaggctttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatg-taattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
| ||| | || || | || | | |||| | || | ||||| ||| | ||| | || | | | |||||||||||||||||| ||||| || |||||||| ||||| || || || || ||||| ||||| || || ||||| ||| ||| ||||| | | ||| |
---------gtgagctcttcttcttctttttc----ttctttctctgcagtgaaatactgttgaatt-gttttcatgatgctgatcgaatcgttcagacagGTTGGAGAACGTACCGCAGGCCAGACGACAAGTCCGGTGGCCACGGAGTTGGCTGGAGCCCCATCATCCCGTACAGCTTCAAAGTTCCAGACGGCTGGGA
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G42010.1 (Glycine max), 3'ss of exon 1
--cataaatctttaggctttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
| |||| || ||||| | | | ||| | | || || | || | | | |||| | || | | || ||||||||||||||| || || || || || || |||||||||||||| ||||||||||| |||||||||||||| || ||| ||| || ||| |||| ||| |
tcgacaaatgttagtttgttggagtgtcagttttgttaatagagaggatcaagatctttaatgaaagtgacataatgtag-gcaagtatt-tgatcagacagGTTGGAGGACCTATCGCAGGCCGGATGAGAAGTCAGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCTGAAGAATGGGA
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G12760.1 (Glycine max), 3'ss of exon 1
--cataaatctttaggct--ttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
|||| || || | | | | || ||| | ||| | | | || || || || | | | |||| | || | || ||||||||||||||| || || || || || || |||||||| ||||| ||||||||||| |||||||||||||| || ||| ||| || || |||| ||| |
taggcaaatgtt-agtttggtagaatgttcattttgttagtag-agaagatcaagattttaaatgaaagtgacataatgtag-gcaagcatt-tgatcagacagGTTGGAGGACGTATCGCAGGCCGGATGAGAAGTCTGGAGGACATGGTGTTGGATGGAGTCCTATTATTCCATACAGCTTCAGAGTGCCCAAAGAATGGGA
upper sequence: AT1G77090.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv18s0001g15360.t01 (Vitis vinifera), 3'ss of exon 1
------cataaatctttaggctttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
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ttgaaacttaaattaacaagctaaagcaactgggtcacttagagctctctctgttgtaaagtgaactgtcacct--tgat-tagtaaagatgt---gctcagacagGTTGGAGGACATACCGGAGACCGGATGAAAAATCTGGAGGCCATGGTGTTGGATGGAGTCCGATTATTCCTTACATCTTTTCAGTCCCTTCTGGTTGGGAMapped 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|124950047|gb|EL025540.1|EL025540EST: GTCTGTCCGAACCTGATGAAGAAG GTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTG
genomic: GTCTGTCCGAACCTGATGAAGAAGgttcgtttca ... gctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTG
EST:
gi|19875594|gb|AU236425.1|AU236425EST: AGGTCTTCTCGCTGGGAGAGTTCCTGGTCTGTCCGAACCTGATGAAGAAG GTTGGAGAACATACCGTAGACCA
genomic: AGGTCTTCTCGCTGGGAGAGTTCCTGGTCTGTCCGAACCTGATGAAGAAGgttcgtttca ... gctcagacagGTTGGAGAACATACCGTAGACCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
taatgtaattgtaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cataaatctttaggctttggacattgattcttggagttgtattatgacagtatagtagttgggaatttgttggtgtaatgtaattgtaatgctcagacagGTTGGAGAACATACCGTAGACCAGACGAGAAGTCAGGAGGGCATGGTGTTGGTTGGAGTCCTATTATCCCTTACGCCTTTTCGGTTCCTCAAGATTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
cataaat
- - - - - - -gctttgg