Sequence
atgc intronic sequence ATGC exonic sequencegtatgtggctacgactttgttctctcaatcaacatataaactggtagtgttgttgcgcgttcttatctgctgaatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03370.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 4
gtatgtggctacgactttgttctctcaatcaacatataaactggtagtgttgttgcgcgt-tcttatctgctg--aatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
||| || | | | | | | | | | | | | | | || | |||| ||| || ||| | | |||||| ||| ||||||| || ||||| ||||| || |||||| ||||| | | |||| ||||||||||||||||||||| ||||| ||||| ||||||
gtaatgcacttatcttctctatttttgagtgaggtgaagtgtcatcctatcttggcctgcctcttttcttatgcaaatttaccatgcagATTGCTGTAAGGTCTCCACACACAAACTCAGCATTCCAGAAGATCTTTTCTTTGCCACCAGAAGAATTTCTAATCAATGATTTTACCTGTCATCTAAAGC
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g10630.1 (Oryza sativa), 3'ss of exon 4
----gtatgtggctacgactttgttctctcaatcaacatataaactg-gtagtgttgttgcgcgttcttatctgctgaatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
| | ||| | || || || || | ||| || | |||| || | | ||| || | ||| |||||| | |||||||| |||| ||||||||||| || | ||||||||| |||| || | |||||||||||| ||| |||| || || ||| | ||||||
gtaagagtttggatggtgtttgtttaattccattgtcggcaaaagtgcgctctgttactgaagttgcatatatg----actgaatactcagATACACCTGCGGTCTGCTCAGACAAATTCAGCGTTCCGTAAGCTCTTTAGTCTTCCTCCAGAAGAATTTCTTATCGATGATTTCACTTGTTATCTAAAGC
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G005195_T01 (Zea mays), 3'ss of exon 5
-----------gtatgtggctacgactttgttctctcaatcaacatataaactggtagtgttgttgcgcgttcttatctgctgaatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
| | | | | || | |||| | ||||| | | || | |||| | |||| | | |||||| | || |||||||||| ||||| | ||| || ||||| ||||| | | |||| |||||||||||| |||||||| ||||| ||||||||||||
gtgataatttcctctcttttcatcaattgtggccagtaatcca-gtataatcctatcttgacaatatattgacttac--acagaattcattctacagATTGCTATGAGGTCTCCTCACACAAACTTAGCATTCCAGAAAATCTTTTCTTTGCCACCAGAAGAATTTCTTATCAATGATTTTACTTGTCACTTAAAGA
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G027665_T01 (Zea mays), 3'ss of exon 4
gtatgtggctacgactttgttctctcaatcaacatataaactggtagtgttgttgcgcgttcttatctgctgaatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
|| | | | ||||| || | || | || | | | || | | |||| | | |||||| | || |||| || || ||||| | ||| || ||||| | ||| | | |||| |||||||||||| |||||| | ||||| ||||||||||||
gtgggaattttctcttttgtcatcaattgtggccagtatcatcctatcttggcaatgtattgacttactcagaattcattctacagATTGCTATGAGGTCCCCACACACAAACTTAGCATTCCAGAAAATATTTTCTTTGCCACCAGAAGAATTTCTTATCAATTATTTTACTTGTCACTTAAAGA
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G39920.1 (Glycine max), 3'ss of exon 5
------------gtatgtggctacgactttgttctctcaatcaacatataaactggt--agtgttgttgcgcgttcttatctgctgaatg-------------gaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
||||| | | |||||| | | || | | | | || || | | | || | ||| || || ||||| |||||||| ||||||||||||||||||||||||| |||||||| |||||||| || |||| || |||||||| ||||||||||| || ||||| || ||
gtaaggatccatctatgttgtctggcatttgtttttatttttaattttttttgtacttctgttttatcacccttttctgtcttctttttgtttttctatttacaaaattgtagATTAATTTGCGGTCTCCTCAAACAAATTCAGCCTTTCAGAAACTCTTTGGGCTTCCACCTGAGGAATTTCTCATCAATGACTTCACCTGTCATTTGAAAA
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G00850.1 (Glycine max), 3'ss of exon 6
------------gtatgtggctacgactttgttctctcaatcaacatataaactggt--agtgttgttgcgcgttcttatctgctgaatg-------------gaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
||||| | | | |||||| | | || | | || | || || | | | || || || || | ||||| |||||||| ||||||||||||||||||||||||| |||||||| |||||||| || |||| || |||||||| ||||||||||| || ||||| || ||
gtaaggatccatctatgttgtcaggcatttgtttttatgtttaattttttttctacttctgttttatcacccttttttgccttctttttctttttctatttacaaaattgtagATTAATTTGCGGTCTCCTCAAACAAATTCAGCCTTTCAGAAACTCTTTGGGCTTCCACCTGAGGAATTTCTCATCAATGACTTCACCTGTCATTTGAAAA
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 4
gtatgtggctacgactttgttctctcaatcaacatataaactggtagtgttgttgcgcgttcttatctgctgaatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
| || || | | | | || | | ||||| |||||||| ||||||||||||||||||||||||| |||||||| || ||||| || |||| || |||||||| |||||||| || || ||||| || ||
---------------------------------------gtcacccttctttctg-acttattcttttgttttaaaaaaattgtagATTAATTTGCGGTCTCCTCAAACAAATTCAGCATTTCAGAAACTGTTTGGGCTTCCACCTGAGGAATTTCTCATCAATGATTTCACCTGTCATTTGAAAA
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G12790.1 (Glycine max), 3'ss of exon 8
gtatgtggctacgactttgttctctc-aatcaacatataaactggtagtgttgttgcgcgttc-ttatctgctgaatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
|||| ||| | |||||||| | || | || | || || | || || | | | ||||| |||||||| |||||||||||||| |||||||||| |||||||| || ||||| || |||| || |||||||| ||||| || || || ||||| || ||
gtattaaaatac--ttatgttctctttggtgtactcctgttttgtcacccttctttctgactcattcttttgttttaaaaaattgtagATTAATTTGCGGTCTCCTCAAGCAAATTCAGCATTTCAGAAACTGTTTGGGCTTCCACCTGAGGAATTTCTCATCAACGATTTCACCTGTCATTTGAAAA
upper sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtatgtggctacgactttgttctctcaatcaac-------atataaactggtagtgttgt------tgcgcgttc-ttatctgctga--atggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
| | ||| | || | | | | || || | ||| | |||| | | | || |||| | |||| | | ||||| || || ||||||||||||||||||| || |||||||| |||||||| || |||| ||| |||||||| |||||||| ||||| |||||||| || |
gtaaatgactagcttttatggtcttaaattcactttgtgaggggactatgtttatgtgttctgactttcttgtctgatttacttgctcattatttcctgatgacattgtatgcagATAAACTTGAGGTCTCCTCAAACAAATTCGGCATTTCAGAAACTCTTTGGACTTCCACCAGAGGAATTTCTCATCAATGATTTTACTTGTCACTTGAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acatataaactggtagtgttgttgcgcgttcttatctgctgaatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
aaatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtggctacgactttgttctctcaatcaacatataaactggtagtgttgttgcgcgttcttatctgctgaatggaaatttcagATTAATGTGCGGTCTCCTCAAACAAATTCAGCTTTTCAGAAGCTCTTTGGTCTCCCACAAGAAGAATTTCTAATCAATGACTTTACATGTCACTTAAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG