Sequence
atgc intronic sequence ATGC exonic sequencegtgagaattaatgataagagatggggctgcttatgtaaatctttgagtttctcattactgatttcctttgggatactgattatgttaatgttatcagTGGAAACTGGGATATAAAGACAAAGATTCCTGAGCAATGCGTAGTTTCAAACATCAATCTTCCGCCATATTTTATGGAGTGGATCAATCTCAAAGACGTC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15140.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G35090.1 (Glycine max), 3'ss of exon 4
--------------------------------------------gtgagaattaatgataagagatggggctgctt--atgtaaatctttgagtttctcattactgatt-tcctttgggatactgattatgttaatgttatcagTGGAAACTGGGATATAAAGACAAAGATTCCTGAGCAATGCGTAGTTTCAAACATCAATCTTCCGCCATATTTTATGGAGTGGATCAATCTCAAAGACGTC
| ||| | | ||| | ||| |||| ||||| | | | | || | |||| || | | | | || | || ||||||||| |||||| | || |||||| | ||| ||||||| | ||| ||||| || | ||||| |||||||||||||||||||| ||||||||||| |||
gtaaatatcattgcttatggtttaccatttatacctcttttcattttcttatttgtagtggtggattattttccttccctgtatatcttgaaatagaagaccagaatttgttcttttacat-caaaatcttttgctattg-cagTGGAAATTGGGATTTGAAAACAAAGGTCCCTCAGCAATGTGAAGTGTCAAAGATAGAGCTTCCTCCATATTTTATGGAGTGGATTAATCTCAAAGATGTC
upper sequence: AT3G15140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S276_83V6.1 (Physcomitrella patens), 3'ss of exon 4
--gtgagaattaatgataagagatggggct--gcttatgtaaatctttgagtttctcattactgatttcctttggga--tactgattatgttaatgttatcagTGGAAACTGGGATATAAAGACAAAGATTCCTGAGCAATGCGTAGTTTCAAACATCAATCTTCCGCCATATTTTATGGAGTGGATCAATCTCAAAGACGTC
| ||| | | || ||| || | | || | || | ||| |||| || ||| || || | | | | | | |||||| ||||||||| | |||||||||||||| |||||||| | |||| ||| | | |||||||| | |||||||| || | || ||| ||
tcatctgaaatggttctaggagtcaaatcttaacacaagtgaggacttcggag---agaaacttgtttcattcaggacttaatggtcaggattgggattgcagTGGCAACTGGGATGTGAAGACAAAGATTCCAGAGCAATGTCGTGATTCAGGTATCGAATTGAAACCATATTTCAATGAGTGGATAAACTTGAAGGACATC
upper sequence: AT3G15140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ31561 (Selaginella moellendorffii), 3'ss of exon 4
gtgagaattaatgataagagatggggctgcttatgtaaatctttgagtttctcattactgatttcctttgggatactgattatgttaatgttatcagTGGAAACTGGGATATAAAGACAAAGATTCCTGAGCAATGCGTAGTTTCAAACATCAATCTTCCGCCATATTTTATGGAGTGGATCAATCTCAAAGACGTC
||| ||| | | || ||| || || || | | ||||||| | | | || || || ||||||||||||||| || |||||||||||||| ||||||||| | || || | ||| ||||| || ||||| || || || ||| |
-------------gtaatagacacagt--cccatttaagctttcga---tcacgct-ctgattttc----gagt----------ttcattttcccagTGGAAACTGGGACATCAAGACAAAGATTCCAGAGCAATGCATCACGTCGGGGATTCCATTGCCGAGCTATTTCTGCGAATGGATAAACCTGAAGGACATT
upper sequence: AT3G15140.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ38589 (Selaginella moellendorffii), 3'ss of exon 4
gtgagaattaatgataagagatggggctgcttatgtaaatctttgagtttctcattactgatttcctttgggatactgattatgttaatgttatcagTGGAAACTGGGATATAAAGACAAAGATTCCTGAGCAATGCGTAGTTTCAAACATCAATCTTCCGCCATATTTTATGGAGTGGATCAATCTCAAAGACGTC
||| || | | || ||| || || | | | ||||||| | | || || || ||||||||||||||| || |||||||||||||| ||||||||| | || || | ||| ||||| || ||||| || || || ||| |
-------------gtaatcgacacagt--cccatttaagctttcgaatcacgct---ctgattttcgtgt--------------ttcattttcccagTGGAAACTGGGACATCAAGACAAAGATTCCAGAGCAATGCATCACGTCGGGGATTCCATTGCCGAGCTATTTCTGCGAATGGATAAACCTGAAGGACATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgagtttctcattactgatttcctttgggatactgattatgttaatgttatcagTGGAAACTGGGATATAAAGACAAAGATTCCTGAGCAATGCGTAGTTTCAAACATCAATCTTCCGCCATATTTTATGGAGTGGATCAATCTCAAAGACGTC
attatgttaatgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagaattaatgataagagatggggctgcttatgtaaatctttgagtttctcattactgatttcctttgggatactgattatgttaatgttatcagTGGAAACTGGGATATAAAGACAAAGATTCCTGAGCAATGCGTAGTTTCAAACATCAATCTTCCGCCATATTTTATGGAGTGGATCAATCTCAAAGACGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA