Sequence
atgc intronic sequence ATGC exonic sequencegtacaatttctttaaaccttttccctatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13445.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5
-------gtacaatttctttaaaccttttccctatccaacattttttttcttacttttgc----ttatactaaatatattcaattg--ttacatcctgc-agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
| || | | || || | | || | | || || || || ||| || || || || | || || | | |||| |||||||||||||| ||||| |||||||||||||| ||||| || || || || || || ||||| || ||||| | |||||||||||||
gtaactatttcaggcttgattaattttcatctgtgcaaatgcctaccattttcattctgtaagattgtacctaa-atgtttaactcatttgcactataccagGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
gtacaatttctttaaaccttttccctatcca-----acattttttttct---tacttt---tgcttatactaaatatattcaattgttacatcctgc-agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
|| | || || | | | | | || ||| | | | ||| || | || ||| || || | | || || | | ||||||||||||||||||| ||||| || ||||||||||| ||||| || || || || || || ||||| || ||||| | |||||||||||||
--gtaactatttcaagcttgcttgattttcatctgtgcatgtgcctaccaaatacattctgtaattgtacctaactgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
gtacaatttctttaaaccttttccctatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
||| | | | || | || || | || || ||||||||| | | | || ||| |||| |||||||||||||||| ||||| ||||| ||||| |||||||||||||| ||||| | || || || |||||||| ||||| | || ||||| |||
--gtaatgccactctagctcacatcaattcat--tcagattgattgtccttgcttatatcagcttgacgca-ttggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
gtacaatttctttaaaccttttccctatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgc-agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
|| || || | || | | | | | | || | | | | || | | | | | ||| | || ||||||| ||||||||||||||||| || |||||||||||||| || || || || ||||| || ||||| || ||||| | ||| |||||||||
--gtaactttttcatacttgtgtacattg----acctgttctttgaacaatatgtacatcagttgc--taagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
gtacaatttctttaaaccttttccctatcca---acattttttttcttacttttgcttatactaaatatattcaattgttacatcctgc-agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
| | ||| | || | ||| | | ||| || ||| | | | | ||| | ||| |||| || ||||||||||||||||| || ||||||||||| || || || || || ||||| || ||||| || ||||| | ||| |||||||||
------------gtagctattttcatactcgtgtacagatctgagctttgaacaatttgtacatcagtcactaagttgctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
gtacaatttctttaaaccttttccc---tatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgc---agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
|| ||| ||| ||| |||| | | | || | | |||| | | | | | | || | || |||| ||||||| ||||||||||| ||||| || |||||||||||||| ||||| || ||||||| |||||||| || || || | |||||||||||||
gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
------gtacaatttctttaaaccttttccc---tatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgc---agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
|| ||| ||| ||| |||| | | | || | | |||| | | | | | | || | || |||| ||||||| ||||||||||| ||||| || |||||||||||||| ||||| || ||||||| |||||||| || || || | |||||||||||||
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------gtacaatttctttaaaccttttccctatccaa--catttt--------ttttcttacttt----------tgctta--tactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
|| || || | || ||| ||| || || |||||| |||||| ||| | || || |||||| | | || || || |||||||||| |||||||| ||||| || |||||||||||||| ||||| ||| | || || |||||||| || || || | |||||||||||||
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttcta---ttttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 6
gtacaatttct----ttaaaccttttcc--ctatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgc---agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
|||||| ||| | ||| ||| | | | || | | |||| | | | | | | || | || |||| ||||||| ||||||||||| ||||| || |||||||||||||| ||||| || ||||||| |||||||| || || || |||||||||||||
gtacaacatctactctgaaaattttatcagttgttttccactctacagaagtagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
---------gtacaatttctttaaaccttttccctatccaacatttttttt--cttacttttgctta--tactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
| | ||||| | | | || | | | | | | || || ||||| |||||| | | | || || || |||||||||| |||||||| ||||| || |||||||||||||| ||||| ||| | || || |||||||| || || || | |||||||||||||
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
---------------gtacaatttctttaaaccttttccctatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
| || || | ||| | || | || | | ||| | || ||||| | | || | || | || ||||||| ||||||||||||||||| || ||||||||||| || ||||| || |||| || |||||||| || || || | ||||||||||||
ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtgatcattgacttattcct----tttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
-------gtacaatttctttaaacctt-ttccctatccaacattttttttcttacttt----tgctta--tactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
| | | ||||| || | || || | | || | | | ||| | || || |||||| | | | || || || |||||||||| ||||||| ||||| || |||||||||||||| ||||| ||| | || || |||||||| || || || | |||||||||||||
aatctttgctggaactgtttaatccatgtttgctgttc--ttttctcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCATATG-CTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------gta--caatttctttaaaccttttccctatccaacattttttttcttacttttgctt-atactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
||| |||||||| | | || ||| | ||||| | | || || ||| | | | | || || || ||||||| ||||||||||| || || || || |||||||| |||||||| ||||| |||||||| ||||| || ||||| | ||| || || ||
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
upper sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------------gtacaatttctttaaacc---ttttccctatccaacattttttttcttacttttgcttatactaaatatattca----attgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
|| | | ||| | || | ||||| | | || | ||| | | | ||| | | | | | | | | | |||||||||| || |||||||||||||| ||||| ||||| |||||||||||||| |||| |||||| | |||||| |||||| | || ||||||
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcc--tagctattgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGTMapped 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|164012634|gb|ES210203.1|ES210203EST: GAAAGTATGCTAGGATTGTGCAGAAATTGGGATTCCCTGCAAAATTCAAG GATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCC
genomic: GAAAGTATGCTAGGATTGTGCAGAAATTGGGATTCCCTGCAAAATTCAAGgtacaatttc ... catcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttttttcttacttttgcttatactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
tactaaa putative branch site (score: 1)
ttatactaaatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaatttctttaaaccttttccctatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT