Sequence
atgc intronic sequence ATGC exonic sequencegtttggccaatacctgtccagactagtttttcttctgtaaacaccatatcatatcaaagctgaacgaatggtttattaatttgatgaatgattaccgttctatgtgttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
gtttggccaatacctgtccagactagtttttcttctgtaaacaccat-atcatatcaaagctgaacgaatggtttattaatt-tgatgaatgattaccgttctatgtg-ttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
| ||| | | ||| || || || |||||||| | || | ||| ||| | || || | | | | | ||| | | || |||||||||| || ||| ||| ||||| |||||||| || || || |||||||| |||||||||||||||||||| || |||||| |||| ||||| || |
--------------agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataat--tttgaaatttgtgttcactaacttgtgttattgataatttgaagGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
upper sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
gtttggccaatacctgtccagactagtttttcttctgtaaacaccatatcatatcaaagctgaacgaatggtttattaatttgatgaatgattaccgttctatgtgttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
| ||| ||| | | | || | || | | || | | |||| | | | || | | | | ||| || |||| |||||| |||| ||||| || || | | ||||| |||||||| || || ||||||||||| ||||||||||||||||| || || |||||| |||| ||||| || |
------ctgctacttgtttctattg--tccgtgactacatgcaataaa-caaacccttgctggcagccctggt-gttcactaactctcttatt-ccattct--gtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
upper sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G07610.1 (Glycine max), 3'ss of exon 7
gtttggccaatacctgtccagactagtttttcttctgtaaacaccatatcatatcaaagctgaacgaatggtttattaatttgatgaatgattaccgttctatgtgttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
| | |||| | ||||| | || | | | || | |||| || | || | | | ||| ||| | | | |||| | |||| ||||| |||||| ||||||| || |||||||| ||||| ||||||||||| || || || ||||||||||| | ||||| |||| || || ||||
-------ctactcctgccttcttgagtttgaaatttgcggaaaagtttgcagttagaagcaaaattactgaaaaacctctataatg-----ttagtgcatttt-tgttttcagGAATGGGTGACAGATAGTCCATTCATAATATCACCTAGAATTACTTTTGAAGTCAGCGTGCGCCTTCTTGGAGGGCTGATGGCCTTGGGATACACAATTG
upper sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G09080.1 (Glycine max), 3'ss of exon 6
gtttggccaatacctgtccagactagtttttcttctgtaaacaccatatcatatcaaagctgaacgaatggtttattaatttgatgaatgattaccgttctatgtgttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
| ||| || | ||||| | || | | | || | |||| || | || | || | || | |||| | | ||| |||| | |||| ||||| |||||| ||||||| || |||||||| ||||| |||||||| || || || || ||||||||||| | ||||| |||| || || ||||
-------ctataactaccttcttgagtttgaaatttgctgagaagtttgcagttagaagcaaaattactg---caaaaactctat-agtgat-agtgcattat-tgttttcagGAATGGGTGACAGATAGTCCATTCATAATATCACCTAGAATTACTTTTGAGGTCAGCGTGCGCCTTCTTGGAGGGCTGATGGCCTTGGGATACACAATTG
upper sequence: AT1G73980.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv17s0000g04650.t01 (Vitis vinifera), 3'ss of exon 5
gtttggccaatacctgtccagactagtttttcttctgtaaacaccatatcatatcaaagctgaacgaatggtttattaatttgatgaatgattaccgttctatgtgttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
| ||| | | | | || | | | || | | |||| | ||| | | || | | | | || |||| | |||| |||||||||||| |||| || || || ||||| ||||||||||||||||||||||| || |||||||| || | ||||| |||| || || ||||
----------tttgtgttttgctgaataatcttttaaagtagaagaaatgcagacgatgctggggtgagggtgaaacga---aatctcttctcaatactgtacttgttttcagGAATGGGTTACAGATAGTCCGTTCATCATTTCACCAAGAATAACTTTTGAAGTTAGTGTCCGCCTTCTTGGTGGCCTGATGGCCTTGGGGTACACAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgaacgaatggtttattaatttgatgaatgattaccgttctatgtgttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
tgttctt CT-rich tract
tttattaatttgatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggccaatacctgtccagactagtttttcttctgtaaacaccatatcatatcaaagctgaacgaatggtttattaatttgatgaatgattaccgttctatgtgttcttagGAGTGGGTTACAGATCGTCCATTTATTATATCACCCAGAATAACTTTTGAAGTTAGTGTTCGTCTTCTTGGAGGATTAATGGCACTGGGTTATACCATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT