Sequence
atgc intronic sequence ATGC exonic sequenceCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttctttctctgctcatcacttctcctaactatttactaacaacaaatggcactcaccagcttatctacgagaag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55810.2 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgtt--ctttctctgctcatcacttctcctaactatttactaacaacaaatggcactcaccagcttatctacgagaag
||||||||||||||||| || | | |||||||||||||| || ||||||||||||||||| ||||| || ||||| |||||||| |||||||||| || | || | ||| | || | | || | | || || || || || |||
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttggcattatttgttggagttagtca--aattactaa--gctcttgattccttgcag--------
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 5'ss of exon 12
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttctttctctgctcatcacttctcctaactatttactaacaacaaatggcactcaccagcttatctacgagaag
||||||||||||||||| || | | |||||||| ||||| || ||||||||||||||||| ||||| |||||||| |||||||| |||||||||| ||| ||| | | | | | | || | | ||| | || || |||
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAGgtttg-gtttaatctacttttgt-attgtttgttggagttaagtcacattactgagctcttgattccttgcag--------
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttcttt-ctctgctcatcacttctcctaact--atttactaacaacaaatggcactcaccagcttatctacgagaag
|| || || |||||||| || | |||||||||| ||||| || || |||||||||||||| |||||| | ||||| |||||||| |||||||| || || | || | ||| || | | | | ||||||| | | | | | |||
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtctgatttatcaacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag---------------
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G169462_T01 (Zea mays), 5'ss of exon 11
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttcttt-ctctgctcatcacttctcctaact--atttactaacaacaaatggcactcaccagcttatctacgagaag
|| || ||||||||||| || || | |||||||| ||||| || || |||||||||||||| |||||| | ||||| |||||||| |||||||| || || | || | ||| || | | | | ||||||| | | || || |||
TGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAGgtctggcttatcaacttttgccatgtgttagggtgagtcaaattactaagatctaa-atttctttgcag---------------
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA02G47270.1 (Glycine max), 5'ss of exon 12
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttctttctctgctcatcacttctcct-------aactatttactaacaacaaatggcactcacca--gcttatctacgagaag--------------------
|| ||||||||||| || ||||| |||||||||||||||| ||||| |||||||| ||||| |||||||||||||| ||||||||||||||||||||| ||| | | || | | | ||| | |||| | | || | || | | | | || || |
TGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtcatctgtgtgtgtgcttgggtatacctgtgtcggattcatttcatgatcactagtgtcttttttttttggtgattcactaacttgtcctttgattattgagcag
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA14G01480.1 (Glycine max), 5'ss of exon 9
------CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttctttctctgctcat---cacttctcctaactatttactaacaacaaatggcactcaccagcttatctacgagaag-----------------------------
|| ||||||||||| || ||| | |||||||||||||||| ||||| |||||||| ||||| |||||||||||||| ||||||||||||||||||||| | | | |||| ||| | | |||| | | || || | || | || | | | ||
TTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtcatttgcgtgtgcttgggtatactgttttgattcatttcatgatcactaac----ttgtcctgttttttttggtgattcactaacttgtcctttgattattgagcag
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA18G08180.1 (Glycine max), 5'ss of exon 12
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgt-tctttctctgctcatcacttctcctaactattt-actaacaacaaatggca-ctcaccagcttatctacgagaag-
|| |||||||||||||| ||| | ||||||||||| ||||| ||||| |||||||| ||| | ||||| |||||||| ||||||||||| |||||| || ||| ||| | | | | || ||| | | | || || || | | || | || ||
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGGttagttcatctgcatctatggtttggtacaaatctctgtttcatttggtgatactgacatcttatgctttgattaatgatcagc
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA08G45270.1 (Glycine max), 5'ss of exon 12
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgt-tctttctctgctcatcacttctcctaactattt-actaacaacaaatggca-ctcaccagcttatctacgagaag
|| |||||||||||||| ||| | ||||||||||| ||||| || || |||||||| ||| | ||||| |||||||| ||||||||||| |||||| || ||| ||| | | | | || ||| ||| | || | || | | ||| | || ||
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGgttagttcatctgcatctatggtttggtacaaatctctgtttcacttggtgatactgatatcttatgctttgatcaatgatcag
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtg----ttctttctctgctcatcact-tctcctaactatttactaacaacaaatg-gcactcaccagc--ttatctacgagaag-----------------------------------
||||||||||||||||| ||| | ||||||| |||||||| |||||||||||||||||||| || ||||| ||||| || || ||||| |||||| | ||| ||||| ||| | ||||| | | || || ||| | ||| ||| ||||||| | |
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag
upper sequence: AT1G55810.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S83_234V6.1 (Physcomitrella patens), 5'ss of exon 12
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttctttc---tctgctcatcacttctcctaactatttactaaca--acaaatgg-cactcaccagcttatctacgagaag-----------------------------------------------------------------------------
||| ||||| |||||||| || || | || ||||||||||||||||| ||||| |||||| |||| ||| | ||||| || ||||| |||||||| | || || || | | || | | || || | || ||| ||||| || | | | |
CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAGgtatcagtcaatttaatcgtgttggatggtgttcactatttttccctgattgtacgaatattcactcttcatttggttcagtaatgatcagtcttagacttccagcgaggtcaacaatgcaactcatcctttgtttaggctgacttaatttttgcactttgcagMapped 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|86074649|gb|DR370406.1|DR370406EST: TCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGATAATGGTCAACAG CTACCCTCAGACATTTCAGAAAGGCATGTGCTTTTACTGGATCCAATCCTC
genomic: TCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttc ... ctacgagaagCTACCCTCAGACATTTCAGAAAGGCATGTGCTTTTACTGGATCCAATCCTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGgtttgtgttctttctctgctcatcacttctcctaactatttactaacaacaaatggcactcaccagcttatctacgagaag
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA