Sequence
atgc intronic sequence ATGC exonic sequence...ttttggttttactttattttctatttttcttcttcagcacatacctgatgcatactttattgtgatattattttttcctatctttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
Basic information
species | Glycine max |
transcript | GLYMA15G04210.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 2
--ttttggttttactttattttc-tatttttcttcttcagcacatacctgatgcatactttattgtgatattattttttcctatctttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
| || | | ||| | ||| | |||||| | | || | | | | | || | || | | || || | | ||||| | ||| |||| ||||||||||||||||| || || || ||||||| |||||| | || ||||| || || || |||||||| |||||||| ||||
gatctttctagaggatgattggaacacctttgtatttcagc---tgcacagtgttctcgtgtatatcccttcatatgctcttgacattccaattaatctgcagGATCGTGATAGTTATTGGAAGATGATGCACAAGTACATAGGGGCAGATGTTACATCACTTGTGACACTTCCGGTCATCATTTTTGAGCCAATGACAATGC
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
ttttggttttactttattttctatttttcttcttcagcacatacctgatgcatactttattgtga--tattattttttcctatc-tttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
| || || || || || | | | | || ||| | | || | ||| | | || ||| | ||| | || || | | ||||| | ||| | ||||||||||||||||||||||| || || |||||||| |||||| | || ||||| ||||| || |||||||| |||||||| ||||
--atcgtagtagtt-atgatccaactatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G114126_T02 (Zea mays), 3'ss of exon 2
-ttttggttttactttattttctatttttcttcttcagcacatacctgatgca-tactttattgtgatattatt-ttttcctatctttgact--tttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
| |||||||| | | |||| | | | |||| ||| | | | | | || | | |||| | | ||| | || | | ||||| | ||| | || ||||||||||||||||| || || || |||||||| |||||| | || ||||| ||||| || |||||||| |||||||| ||||
tctatggttttaaggtcatagtagttttacg-----atcgtatacttgaagttctggtctgattcaggatcactattttaacaaccttgtgtggttaatttgcagGATCGTGATAGCTATTGGAAGATGATGCACAAGTACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 2
ttttggttttactttattttctatttttcttcttcagcacatacctgatgcatactttattgtgatattattttttcctatctttgacttttgtat---acagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
|| | || || || | | | | | | | | || | || || | | ||| |||||||| | ||||| ||||| ||||||||||||||||||| |||||||| || || ||| | || |||||||| || || || ||| |||| ||||| || ||||||||||
--------gtaactaatcgtcgatggtgtctttgatacttcttcttaaattcctctatgtttctctacttacccgaagaaacttatgtttttgtatttaatagGAACGAGATAGTTACTGGAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGC
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 2
-ttttggttttactttattttctattt--ttcttcttcagcacatacctgatgcatactttatt-gtgatattattttttcctatctttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
| | || || ||| ||| | | || |||| || | || || |||||| ||| | |||||| || | || || | | ||||||| || ||||||||||||||||||| || ||||| || |||||||| || |||||||| ||||| |||||| | |||||||| |||||||| ||||
aatcttgtcttgaattacccgatatgaaatcatattttagca-atttatcctgtattttttatttgtgctgatattttgagcttgttctgttttct---tgtagGAAAGGGACAGTTACTGGAAGATGATGCAAAAGTATATAGGTTCAGATGTCACCTCAATGGTGACACTTCCAGTTCTGATTTTTGAGCCAATGACAATGC
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
ttttggttttactttattttctatttttcttcttcagcacatacctgatgcatactttattgtgatattattttttcctatctttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
| || || | || || | | | || | |||| || | | || |||| | | | ||| | | | || | | |||| | || | |||||||| ||||||||||| |||||||| || || || || || ||||| ||||| |||||| | |||||||| || ||||| ||||
-gtaagtcttcccttgttctttttcttgttctttcaatacttgttt---------ttgtttgtttcctcactctttggtctttacga------tcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC
upper sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 2
ttttggttttactttattttctatttttcttcttcagcacatacctgatgcatactttattgtgatattattttttcctatctttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
| || || | || || | | | || | || | || | | || |||| | | | ||| | | | || | | |||| | || | |||||||| ||||||||||| |||||||| || || || || || ||||| ||||| |||||| | |||||||| || ||||| ||||
-gtaagtcttcccttgttctttttcttgttcttttaatacttgttt---------ttgtttgtttcctcactctttggtctttacga------tcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgcatactttattgtgatattattttttcctatctttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
ctttgac putative branch site (score: 4)
ttttttcctatctttg CT-rich tract
atactttattgtgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttggttttactttattttctatttttcttcttcagcacatacctgatgcatactttattgtgatattattttttcctatctttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC
- - - - - - - - - - - - - - cttcttc
- - - - - - - - - - - - - - - - - - -cacatac
- - - - - - - - - - - - - - - - - - - - - - - - -gcatact