Sequence
atgc intronic sequence ATGC exonic sequencegtaactgtcataaccaaacacttacacttgttcttaaaacaaatttaaattgatgtggattacgtgaataaaattgttgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06650.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G045534_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------gtaac-tgtcataaccaaacacttacacttgtt-----cttaaaacaaatttaaattgatgtggatt---acgtgaataaaattg--ttgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG-
|| ||| | | | | || || | || || | | | || | | || | || | | |||| | ||||||||| ||||| |||||||| || ||||||||||| ||||| ||||| ||||| |||||| |||||||||||| | ||| |||| | |
gtgagtcctattctgctgttaattgaatcttcgggtttgctacgcattgattgtaatgtttgggtcttatgttgcagttatatattttcatgttttgaccatttgttatacgtacaagacaagccgttttttaaaatgtgttacattgattcacagGCACACCTTCGACCAGAAGAGGCTTAAGCAGCCACTCTACCGCCACCCATGGGAGGATGTCCTGTACACCAAGTGAG-ATAGAGCCATTCTTTGCAAAGCA
upper sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G002416_T01 (Zea mays), 3'ss of exon 11
---------------------------------------------------------------gtaac-tgtcataaccaaacacttacacttgttcttaaaaca-aatttaaattgatgtggattacgtgaataaaat-tgttgc----------agGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG
|| ||| | | | | || | | | || | | ||||| | | | || |||| ||||| |||| | ||||| || ||||| |||||||| || ||||||||||| ||||| ||||| ||||| ||||| | |||||||||| | | |||| || | |
gtgagtccttgctgttaattgaattctctttggctctgctttgcaatgattgtaatgtttggggtcttatgttgcagtaatatattttcccctattttggccatttgatttacagcaa-gcaacttttctgaaaaaaatgtgttactttgattcacagGCATACCTTCGACCAGAAGAGGCTCAAGCAGCCACTCTACCGTCACCCATGGGAGGATGTACTTTACACCAAGTGAGAAAGCCATTCTTTGCAAGGCATA
upper sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: PP1S46_63V6.3 (Physcomitrella patens), 3'ss of exon 14
--------------------------------------------gtaactgtcataaccaaacactt-acacttgttcttaaaacaaatttaaattgatgtggattacgtgaataaaat-tgttgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG
| ||| || | | | | | | | | | ||| | || || | | | | | | | ||||| || |||||||| |||||| | ||||||||||| |||||||| ||||| ||||| ||||| |||||||||||||| ||||
gtacgtgatcgcacgtgtgttcattgtaaagcttcaacagattgatttgtgtggtatcgttttgcatgatgcattcttccattatcaatgtcgatagaatcctaatgtatccacttattgtcctgcagACATACATTCGACCAGAAGCGTCTGAAGCAGCCTCTGTACCGGCACCCATGGGAGGATGTGTTGTACACCAAGTACACATAA------------------
upper sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: PP1S46_63V6.4 (Physcomitrella patens), 3'ss of exon 14
--------------------------------------------gtaactgtcataaccaaacactt-acacttgttcttaaaacaaatttaaattgatgtggattacgtgaataaaat-tgttgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG-
| ||| || | | | | | | | | | ||| | || || | | | | | | | ||||| || |||||||| |||||| | ||||||||||| |||||||| ||||| ||||| ||||| |||||||||||||| |||| ||| | || |||
gtacgtgatcgcacgtgtgttcattgtaaagcttcaacagattgatttgtgtggtatcgttttgcatgatgcattcttccattatcaatgtcgatagaatcctaatgtatccacttattgtcctgcagACATACATTCGACCAGAAGCGTCTGAAGCAGCCTCTGTACCGGCACCCATGGGAGGATGTGTTGTACACCAAGTACACATAA-ATTCATAACACGATCTAG
upper sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: PP1S35_384V6.1 (Physcomitrella patens), 3'ss of exon 14
------------------------------------------gtaactgtcataaccaaacacttacacttgttcttaa-aacaaatttaaattgatgtggattacgtg--aataaaattgt-tgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG
|| | || | | | ||| ||||| | || || ||| | | | ||| | || || ||||| |||||||||||||||||| | ||||||||||| |||||||| ||||||||||| ||||| ||||||| ||||| | || |||| ||
gtatgtattcacattcgtactcatgatcgatttctttcttatttattttgtattagccattgcttgttacggttctccttagtgaactttaatcaaagatgcttatatttcgtcctgatggtctgcagTCACACATTCGATCAGAAGCGTCTGAAGCAGCCTCTGTACCGTCACCCGTGGGAGGATGTTCTGTACACTAAGTACACGTAAATTTATATCAAGCTCAAA
upper sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: EFJ33298 (Selaginella moellendorffii), 3'ss of exon 15
gtaactgtcataaccaaacacttacacttgttcttaaaacaaatttaaattgatgtggattacgtgaat--aaaattgttgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG
| | ||| ||| | || ||| | | | | | | | | |||||||||||||||||| || |||||| |||| |||||| ||||||| || || ||||| || || | ||| | ||| | |||| |
-----------------------gtaagcttccttccaactgttagaagttgttccagctctcaaactttgacattctttgcagGCACACATTCGACCAAAAGAGATTGAAACAGCCATTGTACCGGCATCCATGGGAGGACGTTCTATACGCTTGATAAAAGGGGAGAGACAGACTTTCCCCT
upper sequence: AT3G06650.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: EFJ15935 (Selaginella moellendorffii), 3'ss of exon 15
gtaactgtcataaccaaacacttacacttgttcttaaaacaaatttaaattgatgtggattacgtgaat---aaaattgttgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG
| | ||| ||| | || ||| | | | | | | | || ||||||||||||||| || |||||| |||| |||||| ||||||| || || ||||| || || | ||| | ||| | ||| ||
-----------------------gtaagcttccttccaactgttagaagttgttccaagctctcaaactttgacattctttacagGCACACATTCGACCAAAAGAGATTGAAACAGCCATTGTACCGGCATCCATGGGAGGACGTTCTATACGCTTGATAAAAGGGGAGAGACAGGCTTTCCCTTMapped 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|164152937|gb|ES071270.1|ES071270EST: GGTTATCTCAACGGCCTCTTCGTCCTCGCTCGATCCATCGGTTTAATCGG GCACACATTCGATCAGAAGA
genomic: GGTTATCTCAACGGCCTCTTCGTCCTCGCTCGATCCATCGGTTTAATCGGgtaactgtca ... attgttgcagGCACACATTCGATCAGAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttcttaaaacaaatttaaattgatgtggattacgtgaataaaattgttgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG
aattgat putative branch site (score: 4)
ttaaaacaaatttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactgtcataaccaaacacttacacttgttcttaaaacaaatttaaattgatgtggattacgtgaataaaattgttgcagGCACACATTCGATCAGAAGAGACTGAAGCAGCCACTGTACCGACACCCGTGGGAAGATGTCTTGTACACCAAGTAATCATATCATTATTCACTTCTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG