Sequence
atgc intronic sequence ATGC exonic sequence...ctgcagggggtaactacttatttgatattgagcttattgtgatttgcgttatgtcattgaacacaatgatgaatgctcaatttatgttcaattgtaacagTTTTTCAGCCAAATGGGCAAGCACCAATATCTTCTACTGACAAGCCACTCAAACAAAATGGCATTGAGGAAGCACAAGTCACACCACCAAGGAGGCTAAG
Basic information
species | Glycine max |
transcript | GLYMA19G09320.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------ctgcagggggtaacta----cttatttgatattgagcttattgtgatttgcgttatgtcattga-acaca-atgatgaatgctcaatttatgt------------tcaattgtaacagTTTTTCAGCCAAATGGGCAAGCACCAATATCTTCTACTGACAAGCCACTCAAACAAAATGGCATTGAGGAAGCACAAGTCACACCACCAAGGAGGCTAAG----
|||| || | | || ||| | || |||| |||| | | |||| ||||| || ||| || ||| ||| | || | |||| || ||||||||||||||||| |||||||||||||| |||||| || | | | | | | | | | | | | || || ||
gtatgttcttgaattgttgggatactatttagacgtgcaaggaattcttgaggtctattttcttgatggaattat-gtgaaggacacaactgatttgatacacagataatgttctctaaatctatctatcctaatattactgatcattacagAATTCCAGCCAAATGGGCAAGCTCCAATATCTTCTACAGACAAGGCATTGACGCCACAAATC--CAAAGCAATGGCTTTGATGTTGCTGAGTT--CTCAGCTCC
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0041g02050.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------ctgcagggggtaactacttatttgatattgagcttattgtgatttgcgttatgtcattga------acaca-atgatgaatgctcaatttatgt---------tcaattgtaacagTTTTTCAGCCAAATGGGCAAGCACCAATATCTTCTACTGACAAGCCACTCAAACAAAATGGCATTGAGGAAGCACAAGTCACACCACCAAGGAGGCTAAG--
| || | | | || ||| || | | || || | | ||| |||| || ||| | || | | ||| | || | |||| || ||||||||||||||||| ||| |||||||||| |||||| || | | | | | | | || | | | | | || |
gtatgttcttgaattgttgggatactatttagacgtgcaaggaattctttaggtctattttgttgttgtaatcatgtgaaggacaaaactgatttgctacacggataatgttttctaattctatctatcctattactgatcattacagAATTCCAGCCAAATGGGCAAGCTCCATTATCTTCTACAGACAAGGCATTGACGCCACAAGTC--CGAAGCAATGGCTTTGATGTTGCTGAGTTCACAGCTCC
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------ctgcagggggtaacta----cttatttgatattgagcttattgtgatttgcgttatgtcattga-acaca-atgatgaatgctcaatttatgt---------tcaattgtaacagTTTTTCAGCCAAATGGGCAAGCACCAATATCTTCTACTGACAAGCCACTCAAACAAAATGGCATTGAGGAAGCACAAGTCACACCACCAAGGAGGCTAAG--
| || || | | ||| |||| | ||| |||| |||| | | ||| ||||| || ||| | || | | ||| | || | |||| || ||||||||||||||||| ||| |||||||||| |||||| || | | | | | | | || | | | | | || |
gtatgttcttgaattgttgggatactactcagacgtacaaggaattctttaggtcttttttgttgttgtaattat-gtgaaggacaaaactgatttgctacacagataatgttttctaattctatctatcctattactgatcatcacagAATTCCAGCCAAATGGGCAAGCTCCATTATCTTCTACAGACAAGGCATTGACGCCACAAGTC--CGAAGCAATGGCTTTGATGTTGCTGAGTTCACAGCTCC
upper sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0041g02010.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------ctgcagggggtaacta----cttatttgatattgagcttat-tgtg------atttgcgttatgtcattgaacacaatgatgaatgct---caatttatgttcaattgtaacagTTTTTCAGCCAAATGGGCAAGCACCAATATCTTCTACTGACAAGCCACTCAAACAAAATGGCATTGAGGAAGCACAAGTCACACCACCAAGGAGGCTAAG--
|||| || | | || |||| | ||| | || || | || || || || | | | ||| || | ||| || | |||| || ||||||||||||||||| ||| |||||||||| |||||| || | | | | | | | || | | | | | || |
gtatgttcttgaattgttgggatactatttagacgtgcaaggaattctttaggtctattttgttgttgtaatcatgtgaaggacaaaactgatttgctacacggataatattttctaattctatctatcctattactgatcattacagAATTCCAGCCAAATGGGCAAGCTCCATTATCTTCTACAGACAAGGCATTGACGCCACAAGTC--CGAAGCAATGGCTTTGATGTTGCTGAGTTCACAGCTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgttatgtcattgaacacaatgatgaatgctcaatttatgttcaattgtaacagTTTTTCAGCCAAATGGGCAAGCACCAATATCTTCTACTGACAAGCCACTCAAACAAAATGGCATTGAGGAAGCACAAGTCACACCACCAAGGAGGCTAAG
aatttatgttcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgcagggggtaactacttatttgatattgagcttattgtgatttgcgttatgtcattgaacacaatgatgaatgctcaatttatgttcaattgtaacagTTTTTCAGCCAAATGGGCAAGCACCAATATCTTCTACTGACAAGCCACTCAAACAAAATGGCATTGAGGAAGCACAAGTCACACCACCAAGGAGGCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- gcagggg
- - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgct