Sequence
atgc intronic sequence ATGC exonic sequencegtgagtattcaattttctgcccttgtcattacgtacttctcccagttcttcaattatctgcccttgtctgatctcacatggttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21410.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os10g10500.1 (Oryza sativa), 3'ss of exon 13
------------------------------------------------------------gtgagtattcaattttctgcccttgtcattacgtacttct-cccagttcttcaattatctgcccttgtctgatctcacatggttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
||| || || || | |||| | || | | | | | | | || | | | || || ||||| ||||| |||| ||| |||||||||||||| |||| ||||| || ||||| |||||||||| || ||||||||||| || || |||| || |
gtaagtaagaatcttctatggaatatgccatgattgagttgtatgacaataagattacatatga-tacatgatatttttttagaactattatattgttttacttaaaacagtaggccattctcattcagttgtgtaactatgtaacagGTATCAGTTTATTCCTCAGCTGATATTCTTGAACAGCTTATTTGGTTACCTTTCACTCCTCATCATTATTAAGTGGTGCACGGGCTCAAAAGCTGACCTT
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 13
-----------------------------------------------gtgagtattcaattttctgcccttgtcattacgtacttctccca----gttcttcaattatctgcccttgtctgatctcacatg-----gttc----cagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
|| | || | | | |||| | | | | | || | | || |||||| || | | |||| | | ||||||| || ||||| ||||||| |||||||| |||| ||||||||| |||| |||||||| || || | ||||| || || ||||||||||| || || |||||||| ||
gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttt-tttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 14
gtgagtatt--caattttctgcccttgtcattacgtacttctcccagttcttcaattatctgcccttgtctgatctcacatggttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
||| | ||| | | || | | | || | | | | | | | || | || ||||| |||||||||||||||||| |||||||| ||| ||||||||||||||||||| ||||||| || ||||| ||| ||||||| || || || || |
----gtaatagcaaaaaacaacttcagtt-taatgaacgtggtgtatggtgtatggtgttcattaattggttttccgatgaggcctcagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 13
gtgagtatt--caattttctgcccttgtcattacgtac-ttctcccagttcttcaattatctgcccttgtctgatctcacatggttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
||| | ||| | | | || | | | || || || | | | | || | ||| | || ||| || |||| |||||||||||||||||| |||||||| ||| ||||||||||||| ||||| ||||||| || ||||| ||| ||||||| || || || || |
----gtaatagcaaaaaacaactttagtt-taatgaacattgtctgtggtgtatggtgttcatcaattggtttttcgatgatgcctc-agGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA12G04330.1 (Glycine max), 3'ss of exon 13
------gtgagtattcaattttctg-cccttgtcattacgtac-ttctcccagttcttcaattatc-tgcccttgtctgatctcacatggttcc-----agGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
| | | |||| | ||| ||| || | || || | | | ||||| | || ||| | | || ||| ||| |||| |||||||||||| |||||||||||||||| | ||| | || ||||| || || || | || || || | |||||| ||||||||||||||| |||||
tctgcaatcaacaatcaaatcactgattctttctatcagttaaactcccttactaattcaacattaatgtacttttttaatttca-atgtttccctctcagGTTCCAGTTCATTCCCCAGATGATATTTCTTAACAGTTTATTTGGTTACCTATCCCTTCTTATTATTGTCAAGTGGGCCACTGGTTCTCAAGCTGATTTG
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA11G12120.1 (Glycine max), 3'ss of exon 13
---------------------------------------------------------------------------------------------------------gtgagtattcaattttctg----cccttgtcattacgtactt--ctcccagttcttcaattatctgcccttgtctgatctcacatggttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
| | | |||| | ||| | ||| | |||| | | | ||| || | || | | || | | | | ||||||||||||| |||||||||||||||| | ||| | | ||||||||||| || | || || || | |||||| ||||||||||||||| |||||
gtaagttaatcggtaatatttatggtaaaatcttactctcgaggatagaaaatagaaatagatggggggggggggggtagttttgtgcagttatttgcatctgcaatcaacaatcaaatcactgattctttctatcagaataaacttacatactaattcaacattaatgtacttttttattcaatgtttccctctcagGTTCCAGTTCATTCCCCAGATGATATTTCTTAACAGTCTATTTGGCTATCTATCCCTTCTTATTATTGTCAAGTGGGCCACTGGTTCTCAAGCTGATTTG
upper sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv03s0038g00290.t01 (Vitis vinifera), 3'ss of exon 13
gtgagtattcaatt--ttctgcccttgt--cattacg-tacttctcccagttcttcaattatctgccc----ttgtctgatc-tcacatg---gttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
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ttcattcttaacttctttctgcagatgtattattagaatccttttggcatgcattaaattgtttgtctaatataggctgttaatcatatgtatgttccagGTTCCAATTTGTTCCCCAGATGATATTTTTAAACAGTTTGTTTGGTTACCTTTCTGTCCTCATCATTGTGAAATGGTGCACTGGTTCACAAGCTGATTTAMapped 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|125273993|gb|EL288078.1|EL288078EST: ATAATGAGCTTCTTTAATGCAAAATTCTTCAAAAGTGCTGTAAACATATG GTTCCAGTTCGTT
genomic: ATAATGAGCTTCTTTAATGCAAAATTCTTCAAAAGTGCTGTAAACATATGgtgagtattc ... atggttccagGTTCCAGTTCGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacttctcccagttcttcaattatctgcccttgtctgatctcacatggttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
atctcac putative branch site (score: 3)
ttcaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtattcaattttctgcccttgtcattacgtacttctcccagttcttcaattatctgcccttgtctgatctcacatggttccagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT