Sequence
atgc intronic sequence ATGC exonic sequencegtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtcttgtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G32790.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------gtgagattttcctcta-------ctatgcaaagtttctgatggttagcgactgaggaaaatgatttagtcttgtc-tatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| | | || | | |||||||| | | | || | | |||||| ||||| | || ||||||||||||||||||||||| ||||| ||||| || ||||| |||||||||
gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G044246_T01 (Zea mays), 3'ss of exon 1
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG---------------------------------
| || | | | | | || | | | | | || || || || | | | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||||||||||||||
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 5
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| || | | | | | || | | | | | || || || || | | | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || |||||||||||||||
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 5
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatt-tagtcttgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| || | | | | | || | | | | | || || || || || | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
gtatgcaaaccttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G069102_T03 (Zea mays), 3'ss of exon 4
-----------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatt-tagtcttgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| || | | | | | || | | | | | || || || || || | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
cttccggaaccgacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagctggttgtttttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G454261_T01 (Zea mays), 3'ss of exon 1
----------------------gtgagattttcctctactatgcaaagtttctgatggttagc--gactgaggaaaatgatttagtcttgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
|| ||| || || | ||| || || || | | | | | || || | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
acatactattgctaccctgtttctgctgtttcaaactgagatactaaggttgtgttgccaatcctacataacatatatacttattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 7
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| || | | | | | || | | | | | || || || || | | | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
gtatgcaaaccttccggaactaacatgcttgtcttaagttcattgctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G457231_T01 (Zea mays), 3'ss of exon 7
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG---------------------------------
| || | | | | | || | | | | | || || ||| || | | | | ||| || ||||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
gtatgcaaaccttccagaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatttgatatggtctctaagaaaattggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGGTTTGGTACCTGCACTCATGCTACTACCACTAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
-------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| | | | | | ||| | | |||||| | | || || || || | | | | ||| || || || |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| |||||||||
tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgata--tggtctctaagaaagttggtcgattttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G349794_T01 (Zea mays), 3'ss of exon 6
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| || | | | | | || | | | | | || || || || | | | | ||| || | ||| |||| ||||| ||||| ||||||||||| ||||||||||| || ||||| ||||||| |
gtatgcaaatcttctagaaccaacatgcatgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctccagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGATG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G014573_T01 (Zea mays), 3'ss of exon 3
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| || | | | | | || | | | | | || || || || | | | | ||| || | ||| |||| ||||| ||||| ||||||||||| || |||||||| || ||||| |||||||||
gtatgcaaaccttctggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctccagCCTGACGATGAACGTGAAATGTGTGCAAGGACAATCTACTGCACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G376619_T01 (Zea mays), 3'ss of exon 6
gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| || || || || | | | ||| || || || |||| ||||| ||||| ||||||||||| |||||||||| || ||||| |||||||||
---------------------------------------gtatctaagaaagttggccgattttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTACACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G398795_T01 (Zea mays), 3'ss of exon 7
---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| || | | | | | || | | | | | || || || || | | | | ||| || | ||| || | ||||| | ||| ||||||||||| ||||||||||| || ||||| |||||||||
gtatgcaaaccttctggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctacagTCTAACGATGAACATGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G324221_T03 (Zea mays), 3'ss of exon 6
-----------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| || | | | | | || | | | | | || || || || || | | | ||| || ||||| |||| ||||| |||| |||||||| || ||||||||||| || ||||| |||||||||
cttccgaaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtttctaagaaagttggttgattttctgtgctctgcagTCTGACGATGAATGTGAAATGTGTGCTAGGACTATCTACTGCACAAACATTGACAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 6
------------------------gtgagattttcctctactatgcaaagt----ttctgatg--gttagcgactgaggaaaatgat-ttagtcttgtcta-tgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
|| ||| | | | || ||| | || || || ||| | | || ||||| || || | | | | |||| ||||||||| || ||||||||||||||||| || |||||||| || || || ||||||
gtgagaaactttgccattatgatcgttttcattttccaaaatttgaaaattggagttttggtgaagtttctctcctaataacatgatgttggtactttggacttcagAATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAG
upper sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------gtgagattttcctctactatgcaa-agtttctga---tggttag--cgactgaggaaaatgatttagt--cttgtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
| | || | ||||| | |||| ||| || | | || | | | | ||||| || | | ||| |||||||||||||||| ||||||||| | || ||||||||||| || || |||||||||
ggaattgtttcatacttgcaacgattgttagtgatatgccatagttcttgaatacggctcggatgaattctggctctaacttagttactctccattacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAGMapped 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|86051671|gb|DR347426.1|DR347426EST: TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGG ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA
genomic: TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGGgtgagatttt ... gtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA
EST:
gi|86081011|gb|DR376768.1|DR376768EST: TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGG ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA
genomic: TACCATCCAAAACAGCTATAGCACCGGTTAACCCGACATTTTTGCCTAGGgtgagatttt ... gtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaaagtttctgatggttagcgactgaggaaaatgatttagtcttgtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
ttctgat putative branch site (score: 3)
tcttgtct putative PPT
aaaatgattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtcttgtctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG