Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaaagtttggttgcttttacttgagtttcatacatctttacctttctataacaatccttgtttcttctgtaagcacaatgttcaatattccttgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25350.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 10
gtaaaaaaagtttggttgcttttacttgagtttcatacatctttacctttctataacaatccttgtttcttc-tgtaagcaca-atgttcaatattcct-tgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG---------
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----------ttaatttgttcaga---gaactttaaa-atccttagctgctt----cagttcatttgctttcatgggaacatgtgtactgataatgtctatatatatcttaacaacagGTTTGATGACACAAATCCAGAAGCCGAAAAGAAAGAGTATATTGACCACATTCAGGAAATCGTACACTGGATGGGATGGGAGCCCTACAAAGTTACATAT
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 10
gtaaaaaaagtttggttgcttttacttgagtttc-atacatctttacctttctataacaatccttgtttcttctgtaagca-caatgttcaatattccttgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG
|| | | | || | ||| ||| | | ||| | || ||| | ||||| | || | | | || ||||||||||||||||||||| || ||||||||| ||||||||||| |||| ||||||||||||||| |||||||||||||| |||| ||||||
----------------aatttctgttaaaattcctataagccttcattagaactttgtaattga-acatgcactataactttctttgttccaagttgatggcttgtggcacttccagGTATGATGATACAAATCCTGAAGCAGAAAAGAAAGAGTATATTGATCACATTGAAGAAATTGTTCAGTGGATGGGTTGGAAACCATTCAAG
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 10
gtaaaaaaagtttggttgcttttacttgagtttcatacatctttacctttctataacaatccttgtttcttctgtaagcacaatgttcaatattccttgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG
| | | || | | | | || || | || | | || || | | | | ||| | | ||||||||||| ||||| || || || |||||| |||| |||||| |||||||||| |||||||| |||||||||||||||||| ||||||
---------------gtctataaatttaaaagttgaatgaactccatttgaaatctgggcctaaattagtaaagaaattttaaattgcttttgtttgtgacttttccactgctagGTATGATGACACAAACCCTGAAGCTGAAAAGAAAGAATATATTGATCATATTGACGAAATTGTCCGGTGGATGGGTTGGGAACCTTTCAAG
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 10
gtaaaaaaagtttggttgcttttacttgagtttcatacatctttacctttct---------ataacaatccttgtttcttctgtaagcacaatgttcaatattccttgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG
| | |||| | | || |||| | | |||| | ||| |||| || | ||| | | | || ||| |||| ||| || ||||| ||||| || |||||| ||||||||||| |||||||||||||||| || | ||||||||||||||||| ||||||
---------------------tcatttgaatcttggactgcttttcttccaccgaaaaaggataaagaagctttaagtttctatagtttctgagtttagttgtgctctgtggctatgtt---agGTTTGACGACACAAACCCAGAAGCTGAAAAGAAAGAGTATATTGATCATATTGAAGAAATCGTCCAATGGATGGGTTGGGAACCTTTCAAG
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ20630 (Selaginella moellendorffii), 3'ss of exon 9
gtaaaaaaagtttggttgcttttacttgagtttcatacatctttacctttctataacaatccttgtttcttctgtaagcacaatgttcaatattccttgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG
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-------------------------------------------------------gtaatcattgaa--ttccactagcaggttcttatgtcttttctacgg----------cagGTTTGACGATACGAATCCAGATGCCGAAAAAGAAGAATATATTGAACACATAAAAGAGATTGTAGAGTGGATGGGTTGGAAACCGTTCAAG
upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ32802 (Selaginella moellendorffii), 3'ss of exon 9
gtaaaaaaagtttggttgcttttacttgagtttcatacatctttacctttctataacaatccttgtttcttctgtaagcacaatgttcaatattccttgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG
|||| ||| ||| |||| | || | || | ||||| ||||||||| |||||||| || ||||| ||||| |||||| | || || |||| ||||| |||||||||||||| |||| ||||||
-------------------------------------------------------gtaatcattgaa--ttccactagcaggttcttatgtcttttctacgg----------cagGTTTGATGATACGAATCCAGATGCCGAAAAAGAAGAATATATTGAACACATAAAAGAGATTGTAGAGTGGATGGGTTGGAAACCGTTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttgtttcttctgtaagcacaatgttcaatattccttgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG
ttttc CT-rich tract
ttcaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaaagtttggttgcttttacttgagtttcatacatctttacctttctataacaatccttgtttcttctgtaagcacaatgttcaatattccttgaaaatctggttttcagGTATGATGATACAAATCCAGAGGCAGAAAAGGAAGAGTATATTAATCATATTGAAGAAATTGTTAAGTGGATGGGTTGGGAACCCTTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA