Sequence
atgc intronic sequence ATGC exonic sequencegtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatttactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52360.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatttactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
| | ||| || ||||| || | || | | | || | || | | | | | || | ||||| ||||||||||| |||||||| || || ||||| ||||| || || || || |||||||| | ||||| || ||||||||||| |||||||| || || || |
---gttttttttttctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtg------tggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G443953_T01 (Zea mays), 3'ss of exon 8
gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatt--tactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
||| | || | || |||| ||| || || || ||| ||| ||| | | ||||| |||| ||||| || |||||||| || ||||| || || || || || || |||| ||||| ||||| |||||||||||||| ||||||||||| ||||| |
--------------------------gtatgacatgttcat-ttgcacat-atgagcattttggacattatgactgattggttaacttgaattagGTTTGGGATTATCAAACAAAGAGCTGTGTTCAAACACTTGAAGGACATGCACATAATGTCTCTGCTGTATGTTTCCATCCTGAGCTTCCAATAATAATGA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 7
gtatgcctcctgttcaatggtcttttagttgatacatttctactggacat-tatgtgctttcaggttat-ttactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
||| ||| | | | ||| || ||| ||| ||| || | | | | ||| | || ||| ||||| ||||||||||||||||| || || || || || || || || || |||| ||||| ||||| ||||||||||| |||||||| || || ||||| |
-------gtttgtcatatgatgcactgaattgtac---tcctgtggtcatgcatgcactctgtgatgacattattggtcaaat---------cagGTTTGGGACTACCAAACAAAGAGCTGCGTTCAAACACTTGAAGGACATGCACATAATGTTTCTGCTGTATGTTTCCACCCAGAGCTACCTATAATAATTA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 7
gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatttactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
| | || | | | ||| | | || || | | || || | | | | | | | || |||||||| ||||||||||| ||||| || ||||| || || || || || || |||| ||||| || || |||||||||||||||||||| || || || || |
---------gtttgtcataagcactgaattg---tactcctgt--gatcatgtctgtactctgtacactgatgacatta-ttgatcaaatcagGTTTGGGACTACCAGACAAAGAGCTGTGTTCAAACACTTGAAGGACATGCACATAATGTGTCCGCTGTATGTTTCCATCCAGAGCTACCTATAATTATTA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 7
-gtatgcctcc---tgttcaatggtcttttagttgatacatttctac-tggacat-------tatgtgctttcaggttatttac-tagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
| || | | |||| || ||| | | | ||| | ||| | |||| ||| | | | | | || | | |||| | |||||||||| ||||| || || || ||||||||||| |||||||| || || |||||||||||||||||||| ||||| || ||||| || ||||| || || || |
gttttgttttcatttgttgcttgatctatctgcttgtacgcatttacatatacatacatatatatatatatgaaaaggaataacatggatgaaacttatgaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 7
--------------gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatttactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
| || | | || | |||| | || || ||| || | ||||| | | || |||||||||| ||||| || ||||| ||||||||||| ||||| || || || |||||||||||||||||||| ||||| || ||||| || || || || || || |
gtttgttttctattttctgttttttcctct-tcatcttccctctaatttggtttcctatatttgtatatggataggaattattatgccgataaaacctttgaatcagGTATGGGATTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 7
gtatgcctcctgttcaatggtcttttagttgatacatttctactggacat---------tatgtgctttcaggttatttac-tagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
| | | |||| | || ||| | || || | | ||| | || | | | | || | | |||| | ||||||||| ||||| || || || ||||||||||| |||||||| || || |||||||||||||||||||| ||||| || ||||| || ||||| || || || |
----gttttgttttcatttgttgcttaatctatctgcttgtcgcgcacacgcacacacacacatgtatgaaaaggaataacatggatgaaacttacgaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
------------------gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatt-tactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
|| | |||| |||| | |||| || | || | ||| || | ||||| | | | | || | |||| ||||| |||||||| ||||| ||||||||||| ||||| || || || |||||||||||||||||||| || || || ||||| || || || || || || |
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtg----tatatggataggaattattatgccaataaaacctt-tgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 7
gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatttac-tagttgaatttcgtgaat-cagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
| || | ||| || | ||| | | ||| | | | || | ||| || | | | | ||| ||| ||||| |||||||| ||||| ||||||||||| ||||| ||||| || |||||||||||||| |||||||| || |||||||| || ||||| || ||||| |
----gtctgccgtt-gataattattttcaagctgtgtttagtatttatgcggtttgatagaaggaaatgttcatggacaaatcctccaaatgcagGTGTGGGACTATCAAACCAAAAGTTGTGTCCAGACACTGGAAGGCCACACACACAATGTTTCTGCAGTCTGCTTCCATCCTGAACTTCCCATAATAATAA
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 7
--gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatttactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
|| | || || | | || ||| | | ||||| | || | || || || | | | | | | | ||| ||| | ||||| |||||||||||||| ||||||||||| ||||| || || || |||||||||||||| ||| |||| |||||||||||||||||||| ||||| | |
gtgtttatctgatgcttattgactaaatagct--tccatttatg-tgcattccatttgattac----tttctgtgattaaattttggtggaacagGTGTGGGACTACCAAACCAAAAGTTGTGTTCAGACACTAGAAGGCCACACACACAATGTTTCTTCAGTCTGTTTCCATCCAGAGCTTCCTATTATTTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctactggacattatgtgctttcaggttatttactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
ttatttacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatttactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT