Sequence
atgc intronic sequence ATGC exonic sequence...tgacaaccttggtttagatgacgaaatttggctaatttttgttccttccttcaatgttgttatattttttgtggtatgagattttgggtattatatgcagAACATAGTTCTGACCGAGCTGAGTTCTTGAAGCTCTGCAAGAGAATAGAGTACACAATTCGAGCTTGGTACCTTCTACAGTTTGAGGACTTGATG
Basic information
species | Glycine max |
transcript | GLYMA19G27800.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g70390.1 (Oryza sativa), 3'ss of exon 1
tgacaaccttggtttagatgacgaaatttggctaatttttgttccttccttcaatgttgtta-tattttttgtggtatgaga---ttttgggtattatatgcagAACATAGTTCTGACCGAGCTGAGTTCTTGAAGCTCTGCAAGAGAATAGAGTACACAATTCGAGCTTGGTACCTTCTACAGTTTGAGGACTTGATG
| | ||| | | ||||| | || || | | | | | || || || || || | | | | ||| | || || |||||| |||||| ||| || |||||||||||||||||||| || |||||||| ||| | || ||||| | ||| |||||||| || |||||
tagtttctacattttgaa--gcaaaattagtct--ttctggatatatgaggagactgtgctactacttactgaaatttaaaaactgtttacctgtttcttgaagAACAACAATCTGACAGAGAAGAATTCTTGAAGCTCTGCAAGAGGATTGAGTACACCATTAGGGCCTGGTATCATCTCCAGTTTGATGATATGATG
upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g29550.1 (Oryza sativa), 3'ss of exon 1
--tgacaacctt-ggttta-gatgacgaaatttggctaatttttgttccttccttcaatgttgttatattttttgtggtatgagattttgggtattatatg--cagAACATAGTTCTGACCGAGCTGAGTTCTTGAAGCTCTGCAAGAGAATAGAGTACACAATTCGAGCTTGGTACCTTCTACAGTTTGAGGACTTGATG
| |||| || |||||| | | | | ||| | || | || | || | || || || || | |||||| | | | ||| |||| ||| || ||||| |||||||||||||||| || |||| || |||||||| || ||||||||||| ||||| || || ||||| || |||
tttttcaacttttggtttatgctaatggaatgtatggaaaagaactgtaatcttagaaattctttccatattc------attaaattttgtgcaattcatggtcagAGCATGATTTGGACCGTTCTGAGTTCTTGAAGCTATGTAAGAAGATCGAGTACACCATCCGAGCTTGGTATCTTCTCCAATTCGAGGATTTAATG
upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G527387_T01 (Zea mays), 3'ss of exon 1
----tgacaaccttggtttagatgacgaaatttggctaatttttgttccttccttcaatgttgttatattttttgtggtatgagattttgggtattatatgcagAACATAGTTCTGACCGAGCTGAGTTCTTGAAGCTCTGCAAGAGAATAGAGTACACAATTCGAGCTTGGTACCTTCTACAGTTTGAGGACTTGATG
|| ||| || | || |||| |||| | | || ||| | | | | | || || || | | | | |||| | | ||||| |||||||| ||||||| || ||||| | ||||||||||| || |||||||||||||| |||||||| || | |||
tccatgttgaccctgatactatctgtaaattttga--aattgaaacggcgtgatttaatttatcttgacataacgca-cataagcccctgatttat-tcttcagAGCGTGAGAACGACCGGACTGAGTTCATGAAGCTATGTAAGAGGGTGGAGTACACAATCCGCGCTTGGTACCTTCTGCAGTTTGATGATCTCATG
upper sequence: GLYMA19G27800.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0068g01000.t01 (Vitis vinifera), 3'ss of exon 1
-tgacaaccttggtttagatgacgaaatttggctaatttttgttccttcct-tcaatgttgttatatttt-ttgtggtatgagattttgggtattatatgcagAACATAGTTCTGACCGAGCTGAGTTCTTGAAGCTCTGCAAGAGAATAGAGTACACAATTCGAGCTTGGTACCTTCTACAGTTTGAGGACTTGATG
|| || ||| | | || | ||| || | ||| | | | | | |||||| | |||| |||| ||| | ||||||||||||||||||||| || ||||| || ||||| ||||||||| | || |||||||| ||||||||||| ||||||||||||||||| |||||
acagcatccatggctcaaatagtgttattgaaggttttggcgatccatgagatttagctcatgatatttgactaaaccttgagttttta---attttgtgcagAACATAGTTCTGACCGTGCCGAGTTTTTAAAGCTGTGCAAGAGAGTTGAATACACAATACGAGCTTGGTATCTTCTACAGTTTGAGGATCTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccttcaatgttgttatattttttgtggtatgagattttgggtattatatgcagAACATAGTTCTGACCGAGCTGAGTTCTTGAAGCTCTGCAAGAGAATAGAGTACACAATTCGAGCTTGGTACCTTCTACAGTTTGAGGACTTGATG
aatgttgttatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgacaaccttggtttagatgacgaaatttggctaatttttgttccttccttcaatgttgttatattttttgtggtatgagattttgggtattatatgcagAACATAGTTCTGACCGAGCTGAGTTCTTGAAGCTCTGCAAGAGAATAGAGTACACAATTCGAGCTTGGTACCTTCTACAGTTTGAGGACTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- acaacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtatga