Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaaccgttacttccatcttctgaaaatatctaatattgatttcactctataaaatttcctaattctttgttttggtgtagGTACATTGCCTGGATTTTAGTTGCAGCTTTGTATCATCTTCCTAATTTTCAGTCAATGGGTTTGGATTTGAGGATGAATTTGTCCTTGTTTCTAACAATT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11800.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G018356_T01 (Zea mays), 3'ss of exon 1
gtaagcaaccgttacttccatcttctgaaaatatctaat--attgatttcactctataaaatttcctaattctttgttttggtgtagGTACATTGCCTGGATTTTAGTTGCAGCTTTGTATCATCTTCCTAATTTTCAGTCAATGGGTTTGGATTTGAGGATGAATTTGTCCTTGTTTCTAACAATT
| || | ||| | | || || || || | | | || || ||| ||| || | || | | || ||||| ||||| ||||| || | ||||| | || ||||| || | ||||||||||||||| ||||||||| |||||||| | ||| | || || || |||
----gtaatcattaaccaccttttatgtgaactaatactcaagttataacaaaatatttgattctctgaagctgtttccaaatgcagGTATATTGCATGGATATTCTTGGCAGCACTATACCATCTGCCCAGTTTTCAGTCAATGGGCTTGGATTTGCGGATGAATCTTTCCCTCTTCCTCACCATT
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G36310.1 (Glycine max), 3'ss of exon 1
---------gtaagcaaccgttacttccatct-----tctg----aaaatatctaatattgatttcactctataaaatttcc--taattctttgttt-tggtgtagGTACATTGCCTGGATTTTAGTTGCAGCTTTGTATCATCTTCCTAATTTTCAGTCAATGGGTTTGGATTTGAGGATGAATTTGTCCTTGTTTCTAACAATT
|| |||| || | | |||| | |||| || |||| || | ||| | | | ||| ||| ||||| | | || |||||||| || ||||||||||| |||||| ||||||||||||||| |||||||||||||| ||||| ||||||||||| | || || ||| | || ||
gtgagtttcttagacaactgt-attgccatatatgtgtctgtgctaatatatatatttatgaaat-attttatgggattagaaataattaagcatccattttgcagGTACATAGCTTGGATTTTAGTGGCAGCTGTGTATCATCTTCCTAGCTTTCAGTCAATGGGAGTGGATATGAGGATGAATCTATCTTTATTTTTGACTATA
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G08860.1 (Glycine max), 3'ss of exon 1
---------gtaagcaaccgt--tact-tccatcttctgaaaatatctaatattgatttcac---tctataaaatttcc--taattctttgtt--ttggtgtagGTACATTGCCTGGATTTTAGTTGCAGCTTTGTATCATCTTCCTAATTTTCAGTCAATGGGTTTGGATTTGAGGATGAATTTGTCCTTGTTTCTAACAATT
|| ||| || | || || || | ||| ||||| | | | | ||| ||| ||||| | || || |||||||| || ||||||||||| |||||| ||||||||||||||| |||||||||||||| ||||| ||||||||||| | || |||||| | |||||
gtgagtttcttagacaaatgtattgctatctatgtgtatgtgctattatatatttttatgaaatatttatgggattagaaataattaagcgcccatttttgcagGTACATAGCTTGGATTTTAGTGGCAGCTGTGTATCATCTTCCTAGCTTTCAGTCAATGGGAGTGGATATGAGGATGAATCTATCTTTGTTTTTGACAATA
upper sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------------------------gtaagcaaccgt-tact--tccatcttc--tgaaaatatctaatattgatttcactctataaaatttcctaattctttgttttggtgtagGTACATTGCCTGGATTTTAGTTGCAGCTTTGTATCATCTTCCTAATTTTCAGTCAATGGGTTTGGATTTGAGGATGAATTTGTCCTTGTTTCTAACAATT
||| ||| |||| || || | | | |||| | ||| | || | || | || | || |||| | ||||| | |||||||||||||| |||||| | ||||||||||||| ||||| |||||||| ||||| ||||||||||| | || |||||| | |||||
gtaagtattttgctctcatgtatttcttttgcttgtgtttttattgtacctccacgtgtactcatctatttctaattacaatacaggaaattactcacattgagctaattgtcttggttaacctttttttggcagGTATGTAGCCTGGATTTTAGTGGCAGCTATTTATCATCTTCCTAGTTTTCTATCAATGGGAGTGGATATGAGGATGAATCTTTCTTTGTTTTTGACAATAMapped 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|116416374|gb|EG458966.1|EG458966EST: CCATTTATCCAGAAGACTATCGGACCAAATTATTCAAACTTCAGTCGGTG GTACATTGCCTGGATTTTAGTTGCAGCTTTGTATCATCTTCCTAATTTTCA
genomic: CCATTTATCCAGAAGACTATCAGACCAAATTATTCAAACTTCAGTCGGTGgtaagcaacc ... tttggtgtagGTACATTGCCTGGATTTTAGTTGCAGCTTTGTATCATCTTCCTAATTTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatctaatattgatttcactctataaaatttcctaattctttgttttggtgtagGTACATTGCCTGGATTTTAGTTGCAGCTTTGTATCATCTTCCTAATTTTCAGTCAATGGGTTTGGATTTGAGGATGAATTTGTCCTTGTTTCTAACAATT
tcctaat putative branch site (score: 2)
ttctttgtttt CT-rich tract
taatattgatttcact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaaccgttacttccatcttctgaaaatatctaatattgatttcactctataaaatttcctaattctttgttttggtgtagGTACATTGCCTGGATTTTAGTTGCAGCTTTGTATCATCTTCCTAATTTTCAGTCAATGGGTTTGGATTTGAGGATGAATTTGTCCTTGTTTCTAACAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG