Sequence
atgc intronic sequence ATGC exonic sequence...aacagataagcatccttggattttgttttaatgaggtttttaaccagttgttgctatgattcttgttaaagatgtaatctaatgagatgctcatctttagGGATGAAAATTAAGACTGACACACCTGTTGCAAAGAAGGCTCGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGA
Basic information
species | Glycine max |
transcript | GLYMA11G33480.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 1
aacagataagcatccttgga---ttttgttttaatgaggt--ttttaaccagttgttgctatgattcttgttaaagatgtaatctaatgagatgctcatctt-tagGGATGAAAATTAAGACTGACACACCTGTTGCAAAGAAGGCTCGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGA
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-gttagttcgattccaggaaaatttctatgctgatggattgattttgatcgttgattggtggaatatatttggatttggtgctattgctaagagtttttgtaacagGGATGAAGATTAAGACTGATACACCGATAGCTAAGAAGGCGAGGGAGGGAGTGATGGAGTTTTTGTTGATGAATCACCCTTTGGATTGTCCTATTTGTGA
upper sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 1
---aacagataagcatccttggattttgttttaatgaggtttttaaccag-ttgttgctatgattcttgttaaagatgtaatctaatgagatgctcatctttagGGATGAAAATTAAGACTGACACACCTGTTGCAAAGAAGGCTCGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGA
|||| | | | | | ||| | | || | | || || | ||||| ||| | | || | | | | | |||||||||||| |||||||| ||||| |||||||| ||||| |||||||||| ||||||||| | ||||||||||||| || ||||| |||||||||||
ttggctagatgatctgtatgcagcactatgttattca--ttctggcttggattatttttttgattgttg--acatattagggttttttttttttttttttttagGGATGAAGATTAAGACCAGTACACCAGTTGCAAAAAAGGCCAGAGAAGGAGTAATGGAGTTTCTGCTGATGAATCATCCTTTGGATTGTCCAATTTGTGA
upper sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S170_67V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------aacagataagcatccttggattttgttttaatgaggttttta--accagttgttgctatgattcttgttaaagatgtaatctaatgagatgctcatctttagGGATGAAAATTAAGACTGACACACCTGTTGCAAAGAAGGCTCGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGA
||| | || || | || || |||| ||| || | || | | | | | | | || |||| | | |||| |||||||||||||| | |||||| | || ||||| || | || ||||||||||||||||| |||||||| |||||||| |||||||| ||||| ||
gtctgattccattagttagtaaccctcttttctcagttgcaagctgtttgacatacaattcgtgcggttcttataacttggggtgtgtctaaaagcgggatactaagaggtcgaatggctgaattgcgtatagGTATGAAAATTAAGACCGGTACACCTCTGGCTAAGAAAGCAAGGGAGGGAGTGATGGAGTTTTTGTTGATGAACCATCCATTGGATTGCCCGATTTGCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttgttgctatgattcttgttaaagatgtaatctaatgagatgctcatctttagGGATGAAAATTAAGACTGACACACCTGTTGCAAAGAAGGCTCGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGA
atctaat putative branch site (score: 3)
ctcatcttt putative PPT
taatctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacagataagcatccttggattttgttttaatgaggtttttaaccagttgttgctatgattcttgttaaagatgtaatctaatgagatgctcatctttagGGATGAAAATTAAGACTGACACACCTGTTGCAAAGAAGGCTCGAGAAGGAGTGATGGAGTTTTTATTGATGAATCATCCATTAGATTGCCCAATTTGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - -gcatcct
- - - - - - - - - - - - - - - - - - - - - - - - tgttgct