Sequence
atgc intronic sequence ATGC exonic sequencegtaacaaaacaaacactttttttttatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G26440.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
--------------------------gtaacaaaacaaacactt-------tttttttatctctcagtttccattgatctaaagctttaaat------aaaacgttttgaat----atgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
| | | | ||| | ||||| | | ||| | | || | ||| ||| || || || ||| | |||| | ||||||||||| || |||||||||||||||| || | ||||||||||| ||||||||||| ||||||||||| || || ||||| | || | ||||||
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
-------------------------------gtaacaaaaca--aacactttttttttatctctcagtttccattgatc-taaagctttaaataaaacgtt---ttgaatatgtt------tctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
||| ||| | ||||| | | | ||| | || || | | || || || || |||| || || || | ||||||||||| || |||||||||||||||| || | ||||||||||| ||||||||||| ||||||||||| || || ||||| | || | || |||
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------gtaac----aaaacaaacactttttttttatctc---tcagt----ttccattgatctaa--agctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
| ||| | | | | | ||| || || ||| ||| | || || | || ||| | | || ||| | |||| | ||||||||||| || |||||||||||||||| || | ||||||||||| ||||| || || ||||||||||| || || |||||| | || | |||||
gtaagaatccattgcgctcgatcataaatattggatgacatattttccttgcaactcttaccatcattattgtttgcctaactaaagtcaaaagtgttctgctaattcaatcatgttatgatattaagcatttaatttttttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAG
upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------gtaac----aaaacaaacactttttttttatctc---tcag--------tttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
| ||| | | | | | ||| || || ||| | ||| ||||| | | || || | ||| ||| |||| | ||||||||||| || |||||||||||||||| || | ||||||||||| ||||| || || ||||||||||| || || |||||| | || | ||||||
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgcttattcatctatgttatgatattaagcattt--aattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
gtaacaaaacaaacacttt---ttttttatctctcagtttccattgatctaaagctttaaa--taaaacgttttg--aatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
|||| ||| | || || | | | ||| || | || || | ||| ||||| | |||| | | ||| | ||||||||||| || |||||||| ||||| || || | ||||||||||| ||||| ||||| ||||||||||| || || ||||| || ||| | ||||||
gtaaaaaagttctctgcttaaattctcattgtgtcatttccagttaatattgtttgccaaacttaaaatggtttgttatttctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 5
gtaacaaaacaa---acactttttttttatctctcagtttccattgatctaaagctttaaa--taaaacgttttga-atatgtttc-tattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
|||| || | | | |||| || | | | |||| || || | ||| ||||| | |||| || | |||| | ||||||||||| || |||||||| ||||| || || | | ||||||||| ||||| ||||| ||||||||||| || || ||||| || ||| | || |||
gtaaaaattctatgcttaaattttcattgtggcatattttcagttaatattgtttaccaaacttaaaatggtttgttatttctttcgcctcttagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGTACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCTGAA
upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------gtaacaaaacaaacactttttttt-tatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
|||| || |||||||| | || | ||| | | || ||| || | || || | || | | ||||||||||| ||||| |||||||||||||| || | || |||||||| |||||||| || |||||||||||||| || ||||| | || | ||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------gtaacaaaacaaacactttttttt-tatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
|||| || |||||||| | || | ||| | | || ||| || | || || | || | | ||||||||||| |||||||||||||||||||| || | || |||||||| |||||||| || |||||||||||||| || ||||| | || | ||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
upper sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 7
-----------------gtaacaaaacaaacactttttttttatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
|| | || | | | || ||| | | | || | | | || | | || | ||| | | | |||| |||||||||| || | ||| ||||||||||| | | |||| ||||||||||| |||||||||||||| ||||||| | | ||| | ||
atgcctgtttgttacttgtggtggattct-caatctgactacatttctggctctgctctgttgtcgaagttgtagttaactgatttta----ggggcaattgcagGTGGTATGTCAAGCGATTTTTGCATCCTGATGTGGTGGCACAGTATGAATATATCTTCATTTGGGATGAGGATCTTGATTTGACTCATTTCAATGCGCGGMapped 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|124961155|gb|EL035730.1|EL035730EST: GAATGGTCTAAACGGGCGATACACGTCAGTGTACCTAAGCAAACCAAGTG GTGGTATGCTAAAAGGTTTCT
genomic: GAATGGTCTAAACGGGCGATACACGTCAGTGTACCTAAGCAAACCAAGTGgtaacaaaac ... tctattgaagGTGGTATGCTAAAAGGTTTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
atctaaa putative branch site (score: 3)
tttctatt putative PPT
tttaaataaaacgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaaaacaaacactttttttttatctctcagtttccattgatctaaagctttaaataaaacgttttgaatatgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA