Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgatagccaacttctgttgatctctatattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcctctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36860.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 3'ss of exon 8
----gtgagtgatagccaacttctg--ttgatctctatattttacccaaaatt-tgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcctctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
|||| ||| ||| || | | | | | ||| | || |||| ||| | | | | ||| | || | | | ||||||| || || ||| || || || || | |||||||| || |||||||||||||| |||||||| ||||| |||||| |||||| ||||||
gtaagtgaatgaattccatgctcagaatgtgcatggacgtgttagttggagttacattcctgatctgtcttgaattgagactgt-----tgcatttcatacac--agATTCCAACGAACAGGAATGGGCTGATCGAATACCGAGCACATCCATTCTGGATGCAAAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTAGGTGTT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G017845_T04 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------gtgagtgatagc-caacttctgttgatctcta-tattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatg----tataaat-----gtaactcctct--agATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
|| || | | | | | | ||||| | ||| || || | ||| | | | | | || | ||| | | ||| | ||| || | ||||||| |||||| ||| |||||||| |||||||||||||| || ||| | ||||| || |||||||||||||| ||||| ||||| |||| |
gtaaggatcactttatttaccctgaccgatctgtttatgctataagttttttctgttgaacattttacttgcctgtttgtgctaataaaatctatctccaatatcttggagaatgtgctttctctacatttttcatgattgacatgtttactcttgctaatatctgattacttcttttcagATTCCTACAAATATGAATGGCCTTATTGAATATAGGGCACATCCTTTCTGGGTACAAAAATACTGTCCTTCACATGAAATGGATGGTACTCCGAGGTGCT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G342105_T02 (Zea mays), 3'ss of exon 3
gtgagtgatagccaacttctgttgat-------ctctatattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgt-ataaatgtaactcctctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
|| || | || || ||||| || | | |||| || | | | | | | | | | | | | || | | | ||||||| ||| || | ||| || ||||| || |||| ||||| ||||||||||| |||||||||||||| ||||| |||||| || ||| |||| |
gtaagcactcttcactttgatttgatagatgagcttgaaaatttagtagtaaataatcttgattatccatttggttattcttatttctgatggaattttggtaaccagATTCCCACAGATAAAAATGGCCTCATTGAATACCGGGCCCATCCTTTTTGGATGCAGAAGTATTGTCCTTCCCATGAAAATGATGGTACACCTAGGTGCT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G099328_T04 (Zea mays), 3'ss of exon 7
gtgagt---gatagccaacttctgttgatctctata----ttttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcctctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
|| ||| || | | | | | | ||| || | || || ||| | || | || | ||| || | ||| | || | | ||||||| |||||| || ||| || ||||| || | |||||||| || |||||||| ||||| |||||||| ||||| |||||| ||||||||||| |
gtaagtgccgacaatccaagtttatggatacgcatgaaggtattgatcagaatatatttctgatccgtct---gtataac-tgcaattattatgtcttcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 5
gtgagtgatagccaacttctgttgatctctatattttacccaaaatttgttcccaggttgtac---taagcttaatgtgtatgtataaatgtaactcctc-tagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
| || | ||| | || |||||| | || | ||| || ||| | | || ||| | | | | || | ||||||| ||||| |||||||||| ||||||||||| |||||||| || ||| | ||||| |||||||| || |||||||||||||| |||||||| ||||
----ccttttttgaattagaattgtccactttattttgttctttcaactttttctagttatagatataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G06720.2 (Glycine max), 3'ss of exon 6
gtgagtgatagccaacttctg-ttgatctctatattttacccaaaatttgttcccaggttgtac---taagcttaatgtgtatgtataaatgtaactcctc-tagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
| || || ||| | || |||||| | | || | ||| || ||| | | || ||| | | | | || | ||||||| ||||| |||||||||| ||||||||||| |||||||| || ||| | ||||| |||||||| || |||||||||||||| |||||||| ||||
-----cttttttgaatttagaattgcccactttattttgttctttcaattttttctagttatagatataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
--gtgagtgatagccaacttctgttgatctctatattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcc-tctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
| ||| ||| || | | | | || | | || |||| | || ||| ||| || ||| || | | || | |||| || ||||| ||||||| || ||||||||||| |||||||| || ||| ||||| |||||||| || |||||| ||||||| |||||||| ||||
tcctttttgaattacaaattgtccgctttattttgttctttc--aattttgctagttatagatatacagcgcaat-tgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G38640.3 (Glycine max), 3'ss of exon 3
gtgagtgatagccaacttctgttgatctctatattttacccaaaatttgttcccaggttgtactaagct-taatgtgtatgtataaatgtaactcctctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
| | | | ||| ||| || | | | |||| | | || | | | | ||| | | ||| | | | ||||| || || ||| || ||||||| ||||||||||| || ||||| || ||| | ||||| || || || |||||||||| |||||| |||||||| ||||
cttcatagaacaaaccttaagtttgccttttcaaaaaagaaaaaaatggcagtaagat-acattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGTCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTCCTCGTTGTT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
---gtgagtgatagccaacttctgttgatctctatattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcctcta--gATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
| || | | | || | | | | ||| | || ||| || | |||| || | ||||| | | || | || |||||| ||||| ||||||| | |||||||| |||||||| || ||||||||| |||| ||||| |||||||||| ||||||||||||||||||||
cattttgaagaaactagatgtgcaatg-tatatttgtttcttttgtatgtttttcacaaatgatactg----tagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0023g01030.t01 (Vitis vinifera), 3'ss of exon 7
-gtgagtgatagccaacttctgttg-atctctatattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcctcta--gATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
| ||| | | | || | | | | ||| | || ||| || | |||| || | |||||| | | | | || |||||| |||||| ||||||| |||||||||||||| |||||||| || |||||||||||||| ||||| ||||| |||| ||||||||||||||||||||
tattttgaataaactagatgtgcaatgtatatttgtttcttttgtatgtttttcacaaatgatactg----tagcatcaatgtatttctttcctttttgtacagATTCCAACAAATGCAGCTGGACTTATTGAGTATAGAGCACATCCGTTCTGGATGCAAAAGTACTGTCCCTCACACGAGCATGATGGAACTCCTCGGTGTTMapped 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|86086879|gb|DR382638.1|DR382638EST: AGCATCATCCTAAATGTGATGTTTGCCATAACTTT ATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGG
genomic: AGCATCATCCTAAATGTGATGTTTGCCATAACTTTgtgagtgata ... actcctctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcctctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
atgtaac putative branch site (score: 3)
ctcctct CT-rich tract
tatgtataaatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgatagccaacttctgttgatctctatattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcctctagATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC