Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G01320.2 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
gtaagtttagcactcttgattttaaaagaatcgcgaggttagatgg--tttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
| | | || || | || | | | | | | | | ||| | ||| | | | | ||||| | | | ||| |||||||||| |||||||| | ||||| | ||||| |||||||| |||||||||||||| || ||||| ||||| ||||| ||||| ||||||||||||||
---aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaacct---tttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA07G06160.1 (Glycine max), 3'ss of exon 19
gtaagtttagcactcttgattttaaaa-gaatcgcgaggt-tagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttg---ttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
| | | ||| | | | || | | || | | ||| || | | || || | |||| | || || | | || | ||| | | | |||||||| |||||||| || ||||| | ||||| ||||| || |||||||||||||| ||||||||||| ||||| ||||| || |||||||| ||||||
---tgatgaacacagatagtgtaaagataggttttgaaatattgattacttcatt--ttaatttttcttc---tgatttagccttttat-tacttggatctacaatcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 19
gtaa-gtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
||| | ||| ||| | | | | | | | | || | ||| | ||| || | |||| || | || | | | |||||||| |||||||| || ||||| | ||||| ||||| || |||||||||||||| ||||||||||| ||||| ||||| || |||||||| ||||||
gtattgattaacacagtgtaaag-ataggttttgaaatattgattagttcat---tttaatttttcttctgatttagcgttttattacttggat-ctacaatcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 19
gtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttg-ttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
|| ||| | | | || | | | | | | || || || | | || ||||| | || | ||| | || ||||| || || ||| ||||||| | |||||||| || || |||||||||||||| |||||||| ||||| |||||||| || ||||||||||||||
-----ttaagcgatgtaagacacagaattctatactagcctgtttatccatggcctttttgcttccatttgatttttacccctggccacatttttcattgatcagATATGTAAAACGCGCGCTGTATCTTCTGCATCTCACTTGTGGCCCATCTCATCCAAACACTGCTGCGACATATATCAATGTGGCTATGATGGAGGAAGGC
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttg-ttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
|| ||| | | | | || | | | | | || || || | | || ||||| | || | ||| | || ||||| || || || ||||||| | |||||||| || || |||||||||||||| |||||||| ||||| |||||||| || ||||||||||||||
-----ttaagcgatgtaaaacacagaattctatactatcctgtttatccatggcctttttgcttccatttgatttttacccctggccacatttttcattgatcagATATGTAAAACGCGCTCTGTATCTTCTGCATCTCACTTGTGGCCCATCTCATCCAAACACTGCTGCGACATATATCAATGTGGCTATGATGGAGGAAGGC
upper sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 13
--------------------------------------gtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtt--tttgtt-------agGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
|| || | | | | ||| | | | | ||| || ||||| | || | || ||| || |||||| || |||||||| | || | || | ||||| | | ||||||||| ||||| |||||||||||||| ||||| |||||||||||||||||||| || |||
gtaagttctaatacccaagcacaggtttctttttggagaatggtctaagatcagagtgtctttgagatcgttaatgattagttgttccgatttttgaactggaattatacgggaaggactgccgctcaatttttattttgttggaatgcagATATGTTAATAGAGCTCTCTACTTGCTACATTTAATATGCGGTCCTTCTCACCCAAATACTGCTGCGACATATATCAATGTAGCCATGATGGAAGAGGGTMapped 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|116396583|gb|EG439175.1|EG439175EST: GATCTTGCTGTCTTCTATTATAGACTTCAGCATACAGAGCTGGCTCTCAA GTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCA
genomic: GATCTTGCTGTCTTCTATTATAGGCTTCAGCATACAGAGCTGGCTCTCAAgtaagtttag ... tttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
atctaaa putative branch site (score: 3)
ttgttttt putative PPT
atatgattgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA