Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcttggttcttaaaactgagttttataagtttctgtcctccttttagacgatttttgattgacaacgcatgagccttttgtagAGTGCTGATTTCTTCCGAGCTGATAATCCTGAAGGTGTAGAGGCACGGACTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G07110.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA14G37520.3 (Glycine max), 3'ss of exon 8
-------------gtaaggcttggttcttaaaactgagttttataagtttctgtcctcctttt--agacgatttttgattgacaacgcatgagccttttgtagAGTGCTGATTTCTTCCGAGCTGATAATCCTGAAGGTGTAGAGGCACGGACTGAG
|| || || ||||| | | | | || | | ||||| | |||| || | || || | | || || | | || |||||||||||| |||||||| |||||||||||||| |||||||| | ||||
ttccctggtttatgttag-tttcattcttggactcatgatgt-tatggtactgtcatgctttctaggaaaacttacaatccatgtcatattcttctct-gcagTCTGCTGATTTCTTTCGAGCTGACAATCCTGAAGGTGTGGAGGCACGTAATGAG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 8
-------------gtaaggcttggttcttaaaactgagttttataagtttctgtcctccttttagacgatttttgattgacaacgcatgagccttt-tgtagAGTGCTGATTTCTTCCGAGCTGATAATCCTGAAGGTGTAGAGGCACGGACTGAG
|| || || ||||| || | | | || | | |||| | |||| | || ||| ||| | | | || || |||||||||||| |||||||| |||||||||||||| |||||||| | |||
ttccctggtttatgttag-tttcattcttggaatcatgatgt-tatggtactgttatgctttctaggaaaacttacaatacatgtcatattcttctatgcagTTTGCTGATTTCTTTCGAGCTGACAATCCTGAAGGTGTGGAGGCACGTAACGAG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 16
-------------------------------------------------gtaaggcttggttcttaaaactgagttttataagtttctgtcctcctttt--agacgatttttgattgacaacgcatgagccttttgtagAGTGCTGATTTCTTCCGAGCTGATAATCCTGAAGGTGTAGAGGCACGGACTGAG
|| || || ||||| | | | | || | | ||||| | |||| || | || || | | || || | | || |||||||||||| |||||||| |||||||||||||| |||||||| | ||||
tcatccattgaaatgtcattaaccatgggtgcttgattccctggtttatgttag-tttcattcttggactcatgatgt-tatggtactgtcatgctttctagGAAAACTTACAATCCATGTCATATTCTTCTCT-GCAGTCTGCTGATTTCTTTCGAGCTGACAATCCTGAAGGTGTGGAGGCACGTAATGAG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 14
-----------gtaag-gcttggttcttaaaactgag---ttttataagtttctgtcctccttttagacgatttttgattgacaacgcatgagccttttgtagAGTGCTGATTTCTTCCGAGCTGATAATCCTGAAGGTGTAGAGGCACGGACTGAG
||| | || ||||| ||| || || | || | | | || | || || || |||| || |||||| ||||| |||||||| ||||||||||| || |||||||| | ||||
tgattccctttctaactgttttattcttgaaataaagatgttgcactagcctgtcatgtttccttgggtaatcttaatcacgtaatattc---ttctttgcagTCTGCTGACTTCTTTCGAGCTGACAATCCTGAAGGCGTGGAGGCACGCAATGAG
upper sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 8
------gtaaggcttggttcttaaaactgagtt--ttata-agtttctgtcctcctt--ttagacgatttttgattgacaacg-catgagccttttgtagAGTGCTGATTTCTTCCGAGCTGATAATCCTGAAGGTGTAGAGGCACGGACTGAG
|| | ||| || || || || | || | | || |||| || || || ||| ||| | | ||| | | || ||| ||||||||||||||||| ||| ||||||||||| | ||||| || | ||||
ccaaaagtcactcttttctcaaaatacgaagatagttgcacaattcttgtcatctttgcttttggaattcttggtaaatcacggtacttttttggtgcagACTGCTGATTTCTTCCGAGGTGACAATCCTGAAGGCATGGAGGCCCGCAATGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttctgtcctccttttagacgatttttgattgacaacgcatgagccttttgtagAGTGCTGATTTCTTCCGAGCTGATAATCCTGAAGGTGTAGAGGCACGGACTGAG
gattgac putative branch site (score: 3)
ccttttgt putative PPT
atttttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcttggttcttaaaactgagttttataagtttctgtcctccttttagacgatttttgattgacaacgcatgagccttttgtagAGTGCTGATTTCTTCCGAGCTGATAATCCTGAAGGTGTAGAGGCACGGACTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG