Sequence
atgc intronic sequence ATGC exonic sequencegtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
Basic information
species | Glycine max |
transcript | GLYMA02G35850.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g06200.2 (Oryza sativa), 3'ss of exon 4
-------gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
| ||| | ||| |||| || || | |||||| | || | || |||||| |||||| ||| | |||| ||||| ||| | ||||||||||| |||||||| | ||||| || || || || ||||||||||||||||||| || | ||||||
gttaatatttccttctgtttttttctcatatcctgtttgc--taacacgcctttattttg--tcaagcttatatgtatgtaaaatgttt-------tgcagGTACAAAAAAGGCGTATATATGACATCACTAATGTCCTTGAAGGGATAGGGCTGATAGAAAAGAAGCTCAAGAACAATATCCGTTGGAA-----------
upper sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g33950.1 (Oryza sativa), 3'ss of exon 4
----------gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
||| | | || ||| | || || ||| | ||| | || || | | | ||| || ||| | | |||| | || || | |||||||||||||| ||||| ||||||| | ||| | || ||||||||||| ||||||||||| | |||||
gtatgggtaaaccccccccctctct----ctcattttaacagtcatttcttttcgttagttttgct-----acaggtttatatatggtttc-caacaaaaacagGTTCGGAAACGGCGCATATATGACATAACAAATGTACTGGAAGGAACAGGTTTGATAGAAAAGAAGCTTAAGAACAGAATCCGTTGGAG-----------
upper sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G333591_T01 (Zea mays), 3'ss of exon 6
------gtccctcttttttccaaaata-tattatgaccaaaatatct-gat--atttatt-cttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
| | || | | | | | | || || ||| | | || ||| | | ||| |||| | || | | ||||| |||| || || ||| | ||||||||||| ||||||||| | ||||| || || || || ||||||||||| ||||||| || | ||||||
gatgatattgatgttgactagaggttggtgctttccttttggtaccttgatccagtcatggtttcttttgttaaacatatgcatata-----tagcttttttcagGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA-----------
upper sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G829408_T01 (Zea mays), 3'ss of exon 6
--------gtccctcttttttccaaaata-tattatgaccaaaatatctgat--atttatt-cttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
| | || | | | | | | || |||| | | || ||| | | ||| |||| | || | | |||||| | ||| || || ||| | ||||||||||| ||||||||| | ||||| || || || || ||||||||||| ||||||| || | ||||||
cagatgatattgatgttgactagaggttggtgctttccttttggtacttgatccagtcatggtttcttttgttaaacatatgcgtata----tagctttttca--gGTACAGAAAAGGCGTATATATGACATCACTAATGTTCTTGAAGGGATAGGACTGATAGAAAAGAAGCTTAAGAACAACATCCGTTGGAA-----------
upper sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g02510.t01 (Vitis vinifera), 3'ss of exon 4
--gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
|| | | ||| | || || || | ||||| || | ||||| || |||||| | ||| | | |||| || |||||| |||||||||||||||| |||||| ||||||| |||||||||||||||||||||||||||||||| || | |||||
gtgttcatttttctatttaagtacatg-----tataatataaattacatg--------ctatttta-----atttaaggtcttttatacaa-acagGTTCAGAAGAGGCGGATATATGACATAACAAATGTTCTGGAAGGAATTGGTCTCATTGAAAAGAAGCTCAAGAACAGGATCCGCTGGAA-----------
upper sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S364_42V6.1 (Physcomitrella patens), 3'ss of exon 4
-gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatac------atgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
|| || | | | | | | || | | | | ||||||| | || | ||| || ||| | | |||| |||| |||||||| || || |||||||| || |||||||||||||| || || | |||||||||||||| || || | || |||||
tgtgactgtgtctga-gagagggagagagagtgagttgatttaaatttattatatctagtatctactggctgatagtgttaggaatccgtggttttaccagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA-----------
upper sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S38_356V6.1 (Physcomitrella patens), 3'ss of exon 4
------gtccctcttttttccaaaatatattatgaccaaaa-tatctgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
| | | | | | ||| | | | | || || || | || | | |||| || || || ||| || ||| |||| |||||||||||||||||||| || || ||||| ||||| || ||||| | ||||| |||||||| ||||| |||| |||||
tatgtagcgctgttatcctttcatttatttcaagtaaataactacctctttttaagctgttctctgacatcagacgatgtacaatcttgggtttcac-cagGTACAAAAGAGGAGGATATATGATATTACCAATGTATTGGAGGGAATTGGGTTAATTGAGAAGAAGCTAAAGAATCGAATCAGATGGAA-----------
upper sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ05692 (Selaginella moellendorffii), 3'ss of exon 3
gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
|| || || | | | | | | | | | | | ||| | || || ||||||||||| | ||||| |||||||| || ||||| |||||||| ||||| | || ||||||||| | || ||||||||| |||||
--------------------gtaa-gtgcatgctgcattcagtgtctgtctctttcgcaagctgc-ttcagagaggctttcttctgcctttcagGTGCAAAAGCGAAGGATCTATGACATCACCAATGTGTTGGAAGGAATTGGCTTAATAGAAAAGAAGTTGAAAAACAGAATAAGATGGAA----------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
atctgat putative branch site (score: 4)
tttttccttttttat putative PPT
tctattatacatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatacatgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG