Sequence
atgc intronic sequence ATGC exonic sequenceCAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGCTTGTTTATATGCAGgtgaatcctttagcctcttctggtttagttttctatctctaacacttgaagatgaatgaataaagttgtgacatttgttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G60690.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os10g33960.2 (Oryza sativa), 5'ss of exon 6
CAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGCTTGTTTATATGCAGgtga-----atcctttagcctcttct---ggtttagttttctatctctaacacttga-agatgaatg---aataaagttgtgacatttgttcag---------
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AAAAGACCGCCCATCTTGGTTCCGTGATTGTCGAAGTCTTGAAGTCTTCACAATGTTTCCAGCTGGAAATGGTGGCACGATCGAACTTGTTTACATGCAGgtgagcgttacatcctaacttttttcttgaattaagtatcccatcattaatttttgccacatgcattccctttttatttatcattcttggctttttcgctcag
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G469551_T02 (Zea mays), 5'ss of exon 7
CAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGCTTGTTTATATGCAGgtgaatcctttagcctcttctggtttagttttctatctctaacacttgaagatgaatgaataaagttg-tgacatttgttcag
|||||||| ||||||||||| ||||| ||| |||| |||||||| | || ||||| || ||||| |||||||| || || || |||||||| |||||||| | | | || | || ||| || |||| | | || || ||| | || |||||
GAAAGATCGTCCATCTTGGTTTCGTGATTGTCGGAGTCTTGAAGTCTATACAATGTTACCAGCTGGAAATGGTGGAACCATTGAACTTGTTTACATGCAGgttagctatac-gttgctgatcattacatttgttaaaa--aacaatggtgctcttatatgtagttttggtttttttccttcag
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA12G08080.1 (Glycine max), 5'ss of exon 6
CAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGCTTGTTTATATGCAGgtgaatcctttagcctcttctggtttagtt-ttctatctctaacacttgaagatgaatgaataaagttgtgacatttgtt-cag
|||||||| ||||||||||||||||||||| ||||||| |||||||| |||||||| || ||||| ||||| || || || || |||||||| | |||||||| | | || ||| | |||| | | | ||| | |||| || | || ||||| | |||
TAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAACTTGTTTACACGCAGgtgagcctcaaatttaagacttatttgttggttctgttttttttttttgttcct--atgattatactta----atttgctacag
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G20520.1 (Glycine max), 5'ss of exon 6
CAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGCTTGTTTATATGCAGgtgaatcct---ttagcctcttctggtttagttttctatctctaacacttgaagatgaatgaataaagttgtgacatttgttcag
|||||||| ||||||||||||||||||||| ||||||| |||||||| |||||||| || ||||| ||||| || || || || |||||||| | ||||||| | || ||||| | |||| | | | | ||| || ||| || | || | ||| | |||
TAAAGATCGTCCATCTTGGTTCCGTGACTGTCGGAGCCTAGAAGTTTTTACTATGTTTCCTGCTGGAAATGGAGGAACCATTGAACTTGTTTACACACAGgtgagcctcaaatttaagacttctttgtcagttccgtttttgtttttgttgttcctg--tgagtatactt---aaattgctacag
upper sequence: AT5G60690.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 5'ss of exon 6
CAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGCTTGTTTATATGCAGgtgaatc-ctttagcctctt--ctggtttagttttc--tatctctaacacttgaaga--tgaatgaataaa--gttgtgacatttgttcag-----------------------------------
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CAAAGATCGTCCATCTTGGTTCCGGGACTGTCGGAGCCTTGAAGTTTTCACCATGTTTCCAGCTGGAAATGGAGGAACTGTTGAACTCTTATACACACAGgtaaacgacaatagctttttgatgggagtaaacgacagcattttgaatatctcaaatcttctttgaatatcctgtattgaaattcagcttgtctggactaatgaatacaaacaaaatgcctttcagMapped 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|164232513|gb|EL995188.1|EL995188EST: AATCGAGCTTGTTTATATGCAG ACGTATGCACCAACGACTCTGGCTCCTGCCCGCGATTTCTGGACCCCGAGA
genomic: AATCGAGCTTGTTTATATGCAGgtgaatcctt ... atttgttcagACGTATGCACCAACGACTCTGGCTCCTGCCCGCGATTTCTGGACCCTGAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAAAGATCGGCCATCTTGGTTCCGTGACTGTAGGAGCCTTGAAGTTTTCACTATGTTCCCGGCTGGTAATGGTGGCACAATCGAGCTTGTTTATATGCAGgtgaatcctttagcctcttctggtttagttttctatctctaacacttgaagatgaatgaataaagttgtgacatttgttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT