Sequence
atgc intronic sequence ATGC exonic sequencegtttgttcagagtttattttccatgttctcatcaatatgactattcaatatctggaaaagctgacaatccctctgattctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G26190.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G26190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g47860.2 (Oryza sativa), 3'ss of exon 6
gtttgttcagagtttattttccatgttctcatcaatatgactattcaata-tctggaaaagctgacaatccctctgattctggtaagatgcttag-tatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
| | ||| | | | || | | || | ||| | | || | || | | | | || | | ||||| ||| | | | | |||| ||||| || |||| ||||||| ||||||| ||||||||||| ||||||||||||||||| || ||||| || | |||||||||||||| || ||||
---------------------------------agcttagatatatactcctttgctataccttattatcatatcgtatttgcaataattttgaaatttgtgttcactaacttgtgttattgataatttga--agGAGTGGGTGACCGATAATCCTTTTATCATATCACCAAGGATTACGTTTGAAGTCAGTGTTCGTCTTCTTGGAGGTTTGATGGCATTGGGATATACTATAG
upper sequence: AT1G26190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G147430_T02 (Zea mays), 3'ss of exon 6
gtttgttcagagtttattttccatgttctcatcaatatgactattcaatatctggaaaagctgacaatccctctgattctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
|| | | | | || | | | |||| || | | | | || | | | | || | ||| | | |||||||||| || || | | ||||| ||||||| |||||||| || ||||||||||||||||| || |||||||| | |||||||||||||| || ||||
-------------------------------ctgctacttgtttctattgtccgtgactacatgcaataaacaaacccttgctggcagccctggtgttcactaact--ctcttattccattctgtgttcaaagGAATGGGTGACCGACAATTCTTTTATCATATCACCAAGGATCACTTTTGAAGTCAGTGTTCGTCTTCTTGGTGGTTTGATGGCATTGGGATATACTATAG
upper sequence: AT1G26190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G09660.1 (Glycine max), 3'ss of exon 6
gtttgttcagagtttattttccatgttctcatcaatatgactattcaatatctggaaaagctg-acaatccctctgattctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
|| |||| ||| | ||| | || || | | | | ||| | | | ||| || | | ||| || || || | ||||||||||| || |||| ||| ||||||||||| ||||| ||||| ||||| |||||||| ||||| |||||||| || ||||| ||||||||||||||||
------------------------------atatatatatatatata-tatataccaattctccatacacgatttgaagagaatgaactttttacatggtgttaactaattgatgtcttg---taacttttcagGAATGGGTGACAGATAATCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
upper sequence: AT1G26190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G14110.1 (Glycine max), 3'ss of exon 6
gtttgttcagagtttattttccatgttctcatcaatatgactattcaatatctggaaaagctgacaatccctctgattctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
| | || |||| |||| | | | | | | | | |||| | | || ||| || | | ||| || || | | ||||||||||| || |||| || ||||||||||| ||||| ||||| ||||| |||||||| ||||| |||||||| || ||||| ||||||||||||||||
----------------------------tttgtgttttgcatattatatatatataccaattccccacactt--gatttgtggagaatttttacacggtgttaactaattgatgtctta---taacttttcagGAATGGGTGACAGATAACCCATTTGTCATATCACCAAGAATTACTTTTGAGGTCAGTGTGCGCCTTCTTGGTGGACTAATGGCTTTGGGATACACAATAG
upper sequence: AT1G26190.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0010g01080.t01 (Vitis vinifera), 3'ss of exon 5
gtttgttcagagtttattttccatgttctcatcaatatgactattcaatatctggaaaagctgacaatccctctgattctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
|| || || | | || | | || || | | | ||| | || | ||| ||||| | | | ||||||| ||| |||||||||||||| |||| ||| ||||| ||||| ||||| || || |||||||||||||| || || ||||||||||| ||||| ||||| ||||||||||
--------------------acaccttgtc-tttgtctggtttgttaacttcctaaggtcattttagtccatgagaaatacgcgagacttgcccaatctgatcagt-----tggttctcattt-------cagGAATGGGTTACTGATAATCCATTTGTTATATCACCAAGAATAACTTTTGAAGTCAGTGTGCGGCTTCTTGGTGGGCTAATGGCCTTGGGGTACACAATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
ttagtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttcagagtttattttccatgttctcatcaatatgactattcaatatctggaaaagctgacaatccctctgattctggtaagatgcttagtatctggtgaataactgtggttctggttttgacaaccagGAATGGGTTACGGATACTCCTTTTGTCATATCCCCAAGGATTACATTTGAAGTCAGTGTTCGCCTACTTGGTGGGCTCATGGCATTGGGATACACAATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG