Sequence
atgc intronic sequence ATGC exonic sequencegtaataaactcagctccaagtcttgagaattgtccatgaaatctttctaaggacggatttatttgtttttgcttgtaaaacattccttgtatccaggtatggatgtgagagtgttggttgattcccatattctttttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCAATTGGGCAGTGTTGGCGATATGAGAGAATGACAAGAGGAAGGCGACGTGAGCATTACCAATGGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G46100.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G46100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g51830.1 (Oryza sativa), 3'ss of exon 3
--gtaataaactcagctccaagtcttgagaattgtccatgaaatctttctaaggacggatttatttgtttttgcttgtaaaacattccttgtatccaggtatggatgtgagagtgttggttga----------ttcccatattctttttg--gtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCAATTGGGCAGTGTTGGCGATATGAGAGAATGACAAGAGGAAGGCGACGTGAGCATTACCAATGGAAT
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gtatgcctttttcaactggtttgtttgtggcatgcttgacttacattcatgtttgtggcattttccattaatttctgttgagtgaccgtttcatctttgccatattatgagtttgttctttgaaatgtgatttttcgcttactttttctcctgtctagAAAATCAGTCTCCCTTCCACTGAAATGGTTTACTATAGGACAATGCTGGCGATATGAGCGTATGACAAGAGGAAGACGGCGTGAACATTATCAATGGAAC
upper sequence: AT3G46100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G158228_T01 (Zea mays), 3'ss of exon 2
gtaataaactcagctccaagtcttgagaattgtccatgaaatctttctaaggacggatttatttgtttttgcttgtaaaacattccttgtatccaggtatggat--gtgagagtgttggttgattcccatattctttttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCAATTGGGCAGTGTTGGCGATATGAGAGAATGACAAGAGGAAGGCGACGTGAGCATTACCAATGGAAT
| | | || ||| || | |||| || | |||| | ||| | || ||| ||| | || ||| | | | || ||| |||||||| || ||||||||| |||| |||||| | || || || || |||||||||||| | ||||| |||||||| | || || |||||||||||||||
--------------------------------------------------------gtatgtatgcctttcctaatcgaacaatc-tagtatatatccatgcctccgtcagaatgt-gatt--ttcactgctcttcttctgtctagAAAATCAGTCTCCCTTCCACTGAAATGGTTTACTATAGGACAATGCTGGCGATATGAGCGCATGACCAGAGGAAGAAGGCGGGAACATTACCAATGGAAT
upper sequence: AT3G46100.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g01360.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------gtaataaactcagct--ccaagtcttg-agaattgtccatgaaatct-----ttctaaggacg--gatttatttgtttttgcttgtaaaacattccttgtatccaggtatggatgtgagagtgttggttgattcccatattctttttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCAATTGGGCAGTGTTGGCGATATGAGAGAATGACAAGAGGAAGGCGACGTGAGCATTACCAATGGAAT
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gtactaagatactagttcttctgtatttcattgcttctgctttctgaatgatgtagtgtcaactaaaaaatttgactgttcaaagaattttggttcattcatttatctatttataa---tttttgtatccaggtacagatgccagaat-----ttgatctccatgtttttttctgtccagAAAATCTGTATCTCTTCCATTGAAATGGTTTGCTGTAGGACAGTGTTGGCGTTATGAGAGAATGACAAGGGGACGCCGTCGTGAGCACTACCAATGGAATMapped 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|86072226|gb|DR367983.1|DR367983EST: TTGAGGCCTGAGCTTACACCTTCTTTAGCCAGGCTTGTCATACAGAAAGG AAAATCTGTTTCCCTTCCATTGAAGTGGTTTG
genomic: TTGAGGCCTGAGCTTACACCTTCTTTAGCCAGGCTTGTCATACAGAAAGGgtaataaact ... tttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatccaggtatggatgtgagagtgttggttgattcccatattctttttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCAATTGGGCAGTGTTGGCGATATGAGAGAATGACAAGAGGAAGGCGACGTGAGCATTACCAATGGAAT
ggttgat putative branch site (score: 5)
ttcccatattcttttt CT-rich tract
atattcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataaactcagctccaagtcttgagaattgtccatgaaatctttctaaggacggatttatttgtttttgcttgtaaaacattccttgtatccaggtatggatgtgagagtgttggttgattcccatattctttttggtccagAAAATCTGTTTCCCTTCCATTGAAGTGGTTTGCAATTGGGCAGTGTTGGCGATATGAGAGAATGACAAGAGGAAGGCGACGTGAGCATTACCAATGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA