Sequence
atgc intronic sequence ATGC exonic sequencegtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78920.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 7
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttg---cttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
|| || | ||| | | | ||| | ||| | | | || | ||| | | ||| | | | |||| | | ||||||| |||||||| || || ||||| || |||| ||||| | ||||| || ||||| || ||||| ||||||||||||||||| || ||||||||||
--------------------------------------------agagatgcatctcgaaaatcactttgtattattattattatcctattatgctctgtaacacatgtatacatcagtagtatactaaaagagggctactc--------agGTTGGTGACAATGTTGGAGATTGTGCCGCACGAGGGGCTGACCTTTTTGAGAGCATAGCAGCTGAAATTATCAGTGCAATGATACTCGGGGGAACAATGG
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 7
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
||| | | ||| | || ||| | | | | | | | ||| | | | || || | | || | | | | || || ||||||| |||||||| || || |||||||| |||| |||||| | ||||| || ||||| |||||||| ||||||||||||||||| || ||||||||||
-------------------------------------------aatatttctttgctctacaactttacttgccttgt-tcttgttatcctatagttcatcttt--tgctactatatattcttgtataacaaaagaaa-ctactc--agGTTGGTGACAATGTTGGAGATTGTGCTGCCCGAGGCGCTGATCTTTTTGAGAGCATAGCAGCAGAAATTATCAGTGCAATGATACTTGGAGGAACAATGG
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
|||| | | || ||||| | |||| || || |||||| ||| | || ||| | || || ||| ||| || ||| || || ||||||| ||||||||||| || ||||||||| ||||||||||| | ||||||||||| || || ||||| |||||||| |||||||| |||||||||||||
----------------------gtttataatttccttgact-tgtgctttttg-------tttctttgttta----------tactttttctggtcttgtacttccattggtaccttactggttttaa-----ttttatttta----agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G24120.2 (Glycine max), 3'ss of exon 7
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
| || ||||| | |||| || || |||||| | | | || | | | | ||| ||| | | || || | ||| || || ||||||| ||||||||||| || ||||||||| ||||||||||| | ||||||||||| || || ||||| || ||||| |||||||| |||||||||||||
-----------------------------atttccttgact-tgtgctttt--------gtttctttgtttatactttttctgctcttatacagttatacttccgttggtaccttactggttttga-------tttaatttta----agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATTAGTGCCATGATACTTGGTGGAACAATGG
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
| || ||| | | | ||| | | | | | || | || ||| |||| | || ||| || | ||| || | ||| |||||||||||||||| || || ||||||||||||||||||||| | ||||||||||| || || |||||||||||||| |||||||| |||||||||||||
-----------------------------------------atttgtttcattggtgcatttttcatgtctttgccttttttc---taagggaaaaatgtatgtcctttccataacaagagtttt----ccctcttcttcat-ttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
-----------------gtatttgatctttgt-----tctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
| || | | ||| ||| | || ||| || ||| | | || ||| | || |||| | || ||| | | || ||| | | | | || | | || ||||| | | || | |||| |||||||| ||||| || |||||||| | ||||| ||||||||||||||||| || || ||||| |||||||| ||||| || ||||| || ||||
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgt-tggttctagtcctctctatacttgca-atgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcc---tgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S28_200V6.1 (Physcomitrella patens), 3'ss of exon 7
--gtatttgatctttgttctttttgtttct-tactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgt-cattta--ggcatttaaa-----gccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
| | | | | || ||| | | || || | ||| || ||| | || || || ||| | | | || ||| || ||| ||| || | | || || || | | | | | ||||||||| || || ||||| || |||||||| | ||||| ||||||||||||||||| || || |||||||||||||| ||||| || ||||| |||||||
gtatgctcaaattaatgttattctgtatatgtagttgtctaattttg--attattagac-tggtgtc---agttgtagtgtgttggacactagtagagttcatccacatttgagtacctctattggtcttccagttgctgatgcctgtacatcgaagtagGTTGGTGATAACGTGGGAGATTGTGCTGCCCGTGGTGCCGATTTATTTGAAAGTATTGCAGCTGAAATCATCAGTGCCATGATTCTTGGTGGTACAATGG
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ13082 (Selaginella moellendorffii), 3'ss of exon 6
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgt-tttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
|| ||| || |||| | | || || |||| |||||||||| ||||| || || ||||||||| | |||||||||||||| |||||||| ||||| || || || || || ||||| || || || || ||||
------------------------------------------------------------------------------------------------------gtaaattttgtagtttacgtttagttgatggacttaatggtcttacagGTTGGAGATAATGTTGGTGATTGTGCTGCTCGTGGTGCTGATTTATTCGAAAGTATTGCTGCGGAGATAATTAGCGCCATGATTCTGGGAGGCACTATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
ccattttcatcttctt CT-rich tract
atttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA