Sequence
atgc intronic sequence ATGC exonic sequence...tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73350.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
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----------------------------ctttcttatcgggtgcttcccacgggcatctatgtgc---------aatgttctgataacatgccctgacagggattttggctctct---acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
| || ||| | || | | ||| | | | | |||| ||||| ||||| | ||||||| || | | | ||||| | | | |||||||||||||||||||||| | |||||||| ||||| |||||||| |
------------------------------------tcaaatgactaagcatttccaataggtatcagtgtacaa-tgttcttataacatgccctgacagggattttggttctct---actcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G146786_T02 (Zea mays), 3'ss of exon 2
tatatctttgttagcattagtggttattga-tgtgtg-tgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
| | || || | | || | || || | || ||| | || | | ||| | | | | |||| ||||| ||||| | ||||||| || | | | ||||| | | | |||||||||||||||||||||| | |||||||| ||||| |||||||| |
-tcacacgaggatgccttgcttttacttaaatgcttgatcaaatgactaagcatttccaataggtatcagtgtacaa-tgttcttataacatgccctgacagGGATTTTGGTTCTCT---ACTCGGTGGTTGATACCAACAGATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G33570.1 (Glycine max), 3'ss of exon 2
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
| | ||| ||| || ||| | | || | || ||| |||||||| |||||||||||||||| ||| | | ||| ||| | |||| ||||||||||||||||||| || |||||||| || ||||||||||||||||
-----------------------------tcaactttcaagcaattttt-tgtgcaatt------tgagg---gattttgctgataacatgccccggcagggatattggcttc-ctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 2
---tatatctttgtta-gcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
| | |||| |||| | | | ||| ||| ||| | | | || ||| | || | || || ||| |||||||| |||||||||||||||| ||| | | ||| ||| | |||| ||||||||||||||||||| || |||||||| || ||||||||||||||||
ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttttgtgcaatttgagg----gattttgctgataacatgccccggcagGGATATTGGCTTC-CTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 2
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactc---gacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
| | | || || || || ||| ||| | ||| | | | | | | || ||| |||||||| |||||||||||||||| ||| | | ||| ||| | |||| ||||||||||||||||||| || || ||||| || ||||||||||||||||
--ttgcaaagcagaattttgtaattcttc-tgtatgtcgttttcaactttcaagcaattttttgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTC-CTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G28980.1 (Glycine max), 3'ss of exon 2
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
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-----------------------------tcaactttcaagcaattttt-tgtgcaatt------tgagg---gattttgctgataacatgccccggcagggatattggcttc-ctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 2
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactct-atattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
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----------------------------------------acatctcttctctttttatatgacattctgtggagagttttctgataacatgccccggcagggatcttggcattgcc-taccgggtggttgatgtgagcagATGCAAGAGGTTGCAGGGGAACGTGGAGGTTACCTTCATGGACGAGGCG
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S402_46V6.1 (Physcomitrella patens), 3'ss of exon 2
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTG-CATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
||| || || | | || | | || | | ||| || || | | || ||||||| ||| ||| || || ||||||| ||||| |||||||||||||| || ||||| ||||| ||||| |
----------------------------------tgtttag-aatattgagattcacgtttgctgaggagaacaaaagcgttga----tttccttgtt--gaatgacggcccttgtttattaaaacgttgttatcaagcagATGCAGGAGGTAGCTGGTGAACGTGGTGGATATCTGCATGGTCGAGGAG
upper sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S88_45V6.1 (Physcomitrella patens), 3'ss of exon 3
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCA-TATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
| ||||| || | | || | ||| | | ||| || || || ||| | || | ||| || | ||||||| ||||| |||||||||||||| || ||||||||||| || || |
---------------------------------atctgaaggtatctatgc-tgtggtctggtgagtatactgagggtat----taatttaccttcttagtgatgat--ccttgtt-tattggaacattgcgatggcacagATGCAGGAGGTAGCTGGTGAACGTGGTGGATATCTTCATGGTCGTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
tgataac putative branch site (score: 2)
cttgcccc CT-rich tract
tctatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - tgtttga