Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G06400.3 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
-----------------------gtaagtctctcatcattgtc--cactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
| | ||| | | | || || ||| |||| ||| || | ||| || | ||||||||||||||| ||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgtt-gataa--ttggtg-gttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 11
----gtaagtctctcatcattgtccac-----tgtagtttatgaactttctcttcacgtttgacgagt--ctggca-tattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
||| ||| | ||| ||| ||| ||||| | | | ||| | ||| | || ||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| || || || || ||||||
gtcagtatttctagtagttttgaacacagccatgttatttatatctgtacccaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
gtaagtctctca--tcattgtccactgtagtttatgaactttctcttcacg--------tttgacga-gtctggca-tattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
|| ||| | ||| | || | ||| | ||| | | ||| || |||| || | ||| | || ||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| || ||||||
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
-------------------gtaagtctctcatcattgtccactgtagtttatgaactt---tctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
|| || | | | || || | || | | || | |||| || | | || | ||||||||| ||||| ||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||
gttagtattcttgttgattgtcagcagccttctaacttgcagtgatgcc-ataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctg----------gcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
| | | | || || || | | | | || | | ||| || | ||||| || | |||||||| ||||| || |||||||| || |||||||| ||| ||||||||||||| ||||||||||||||||||||||||||||| |||
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattattt-accaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 11
gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggca--tattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
||| | || | || | || | | | | | | ||| ||| |||||| || |||||||| |||||||| || ||||| || ||| ||||||| || ||||||||||||||||| || ||||| ||||| ||
------------------------gtaata-ataatgatttgttctgagtggcatgtttttagaaattatgctg-cagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG
upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 11
gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctg--gcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
||| || || | | ||| | || | || | | ||| || ||||||| || |||||||| |||||||| || ||||| || ||| ||||||| || ||||||||||||||||| || ||||| ||||| ||
------------------------gtaa--tagtaatgatttgttc-tgagtggcatgttttagaaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAGMapped 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|164095597|gb|ES023167.1|ES023167EST: GTATCAATCTTGCTACTGCAGATGTTGTGATCCTTTACGATAGTGATTG GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGA
genomic: GTATCAATCTTGCTACTGCAGATGTTGTGATCCTTTACGATAGTGATTGgtaagtctct ... attctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGA
EST:
gi|116473628|gb|EG516220.1|EG516220EST: GGTATCAATCTTGCTACTGCAGATGTTGTGATCCTTTACGATAGTGATTG GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCN
genomic: GGTATCAATCTTGCTACTGCAGATGTTGTGATCCTTTACGATAGTGATTGgtaagtctct ... attctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtagtttatgaactttctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
gtttgac putative branch site (score: 4)
tttatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT