Sequence
atgc intronic sequence ATGC exonic sequencegtattggtgtttccatctttctcttttataatgttctcgtcccatgggtttcctgatgatactgctttcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G38510.5 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 3
---------------------gtattggtg-tttccatctttctcttttataa-------tgttctcgtcccatgggtt-tcctgatgatactgctttcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
| || | | |||| | | || | | || | | || ||| || | | || | | | ||| ||||| || || |||||||||||||| || ||||| ||||| ||||| || || || ||||||||||| || |||||||||||||| ||||||||||| |||
gtgtgtacagttttctccaatatgatgataactaccatgtagattttgaacagctcagtctgctagcctcttatgctttgttcctttgcttgcatatccatctatagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAG
upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 2
---------------------------------gtattggtgtttccatctttctcttttataatgttctcgtcccatgggtttcctgatgatactgctttcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
|| | | ||| | | | || | | | | ||||| || | || | | || ||||| || || |||||||||||||| || ||||| ||||| ||||| || | || ||||||||||| || ||||||||||| || ||||||||||| |||
gtaaaggtgtgcacagttttctccaatatgatgctaactaccctgcagattttgaacagctcattctgctagcctcttatacttcctt-tgcttgtgtatccatcattagggcccaaagtaccaaGAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAG
upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 3
---------------------------gtattggtgtttccatctttctcttttataatgttctcgtcccatgggtttcctgatgatactgctttcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
|| | | ||| | | | || | | | | ||||| || | || | | || ||||| || || |||||||||||||| || ||||| ||||| ||||| || | || ||||||||||| || ||||||||||| || ||||||||||| |||
gtgtgcacagttttctccaatatgatgctaactaccctgcagattttgaacagctcattctgctagcctcttatacttcctt-tgcttgtgtatccatcattagGGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAG
upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G42940.1 (Glycine max), 3'ss of exon 3
---------------------------gtattggtgtttccatctttct--cttttataatgttct--cgtcccatgggtttcctgatgatactgctttcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
|| || |||| || | ||| ||| |||| || | |||| | |||||| || |||| || |||| ||||| ||||| ||||| ||| | || ||||||||||| || ||||| |||||||| || |||||||| || |||||||||||||||
gtaatgatggtgtgctagttgatatttttaatgaattttctggtattttggttttctcaatattctgctgtgactaaagtttatattttatactgaaactgcatc-agGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG
upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 4
------------------------------gtattggtgtttcca--tctttctcttttataatgttct--cgtcccatgggtttcctgatgatactgctttcct-ctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
||||| |||| | ||| ||| |||||||| || | |||| | |||||| | || | |||| || |||| ||||| ||||| ||||| ||| | || ||||||||||| || ||||| |||||||| || |||||||| || || ||||||||||||
gtaatgatggtgtgccgcttgctgatattgttattgaattttctgggttttttattttctcaatgttctgctgtgactaaagtttatattttatactgataaactgcatcagGGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGCGAAAAGGCTGTTGTTCAG
upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 3
----------------------------------------gtattggtgtttcca-tctttctcttttataatgttc--tcgtcccatgggtttc--ctga---tgatactgctttcctct-ctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
| | ||| || |||||| | | ||| | | || ||| | || | || ||| | ||| |||| ||||| | ||||| ||||| ||||| || | || ||||||||||| || ||||| ||||| || ||||||||||| || || ||||||||||||
gtaatgactgtagtgtgatactcctctgtatgctatgcttattctaaaattttcaacttttctcaatgaagatgaccaactattttttgtgttgtgaccgagttttatgctgatcaactccatcagGGACCTAAGTTTCAAGAGATTGTTAATATTCGCTTGGGAGATGGAACTACTCGGCGTGGACAAGTGCTAGAAGTTGATGGTGAAAAGGCTGTTGTTCAG
upper sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 3
------------------gtattggtgtttccatctttctcttttataatgttctcgtcccat--gggtttcctgatgat--actgctttcct-----ctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
||||| | ||| |||||| || ||| || | || | | | | |||| | | | || || | | |||| || ||||| ||||| ||||||||||| ||| | || |||||||| || |||||||||||||| || ||||||||||| |||||||| ||||| |||
gtattcctcacttatttagtatttttatttattcctttctgattcatatgatttccatctgttcagaatctattgatcaatgattttctttctaattgcaccagGGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGMapped 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|86066801|gb|DR362558.1|DR362558EST: GAACTGTTTCTGGTGTTGCGGGACCTCTCGTCATCCTTGAAAAAGTCAAG GGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACC
genomic: GAACTGTTTCTGGTGTTGCGGGACCTCTCGTCATCCTTGAAAAAGTCAAGgtattggtgt ... tcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttataatgttctcgtcccatgggtttcctgatgatactgctttcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
tcctgat putative branch site (score: 3)
tactgctttcctctct putative PPT
ataatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattggtgtttccatctttctcttttataatgttctcgtcccatgggtttcctgatgatactgctttcctctctagGGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT