Sequence
atgc intronic sequence ATGC exonic sequence...tcaccccatatttcagtacaaaaaattcccttgatatcttgatcagaacttattgttgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
Basic information
species | Glycine max |
transcript | GLYMA12G30520.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 12
tcaccccatatt-tcagtacaaaaaattcccttgatatc-ttgatcagaacttattgttgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
| | | | ||| | | | || | || | ||| | |||| || | || | || ||||| | | | |||| || |||||||| ||||| ||||| || | || ||||| || || |||||||| |||||||| ||||||| ||| ||||| || ||||| || |||||||||||
-agttctgaactacctgtaggatagtaactctagctagcattggactagttttatgtgaaattgatgatttccaccaatatc-taactttttttttctatagGTATGTCGATGTTATTCTGCAGCTGATAGACAAAGCAGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTCACCAACAATGAAGAT
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 13
--tcaccccatatttcagtacaaaaaattcccttgatatcttgatcagaact-tattgttgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
|| | || | ||| | || || || | | | || | | | | || ||||| | | ||| | |||||||||||||| ||||||||| | || ||||| || || |||||||| |||||||| ||||||| ||| ||||| || |||||||| ||||| ||||||
aacaactgtagcaaattgtgttgtcagttctgtgtgcattttaatttatgcaatttcgtcaccattgagtttttgct-atatctgat--ttgtatttgtgtagGTATGTTGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGAC
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 12
------------------------tcaccccatatttcagtacaaa----aaattcccttgatatcttgatcagaacttattgttgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
| ||| ||| | || | | | | || | | | ||| | | | | | ||| || | ||| | | | || | ||||||||| |||||||| ||||| || || |||||||| || |||||||| || |||||||| |||||||| |||||||||||||| ||||| |||||||||
gtaaagagaactcgacaagaagtatatgtacattttttcatgcacactatagagacatgtgctgtgccctttagatcct--tacacaagcaat-tggtcaaagatgttaattttgatgttct---cagGTATGTAGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATTTGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G22770.2 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------tcaccccatatttcagtacaaaaaattcccttgatatcttgatcagaacttattgttgatgtaatatgtatactgatatcatgtcatccct--tttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
| | || |||| |||| || | | || ||| | || ||| | || || | | | | |||| | | | | | |||||||||||||||||| ||||| || || |||||||| || |||||||| || ||||||||||||||||| |||||||||||||| ||||| |||||||||
gtgaggataactcgatacgaagtatatgtacacttcattcatgcacacaaatttggttacagtaacatgcattatccatttggtgtgacctttagatccttgcaaatcaactggttaaag-atgttaattttgatgttttcagGTATGTTGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGAC
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 12
tcaccccatatttcagtacaaaaaattcccttgatatcttgatcagaacttattgttgatgtaatatgtatactgatatcatgtcatccctt-ttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
| ||| | || | | |||| | || | | ||| ||| || || || || || | || ||||||||| || ||||| || || || ||||||||||| || ||||||||||||||||||||||||||||| || || ||||||||||||||||||||||||
-gtgctttcattggaaggttggaagcaattgttgcctgttgaagcaacaagatcttctactgtttatatatgttgtcatgtattcttcaattgtcatgcagGTATGTGGACGTGATCCTACAGTTGATTGACAAGGCAGGAGATTTTGTCAGTGATGACATATGGTTTCGTGTTGTGCAGTTTGTTACAAACAATGAAGAC
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S26_36V6.1 (Physcomitrella patens), 3'ss of exon 12
tcaccccatatttcagtacaaaaaattccct-tgatatcttgatca---gaacttattgt-tgatgtaatat-gtatactgatatcatgtcatcccttttat-acagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
| | || || ||| | ||| | ||||| | |||| | | | ||| || || | || | | || | | | || |||||| |||||||| || | || | ||||| ||||| ||||||||||| |||||||| ||||||| || |||||||| |||||||| |||||||| ||
------ttgaccttgatatggaatgttcattgtgagttattgattacctagacttctagaatactgtgctaaagtgaagtgct-ttatattgtgattgggatcgcagGTACGTTGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGAT
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 12
tcaccccatatttcagtacaaaaaattcccttgatatcttgatcag---aacttattgt-tgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
| | | ||| | | | | | || | |||| ||||| | || |||| | || | | | || | |||||||| ||||| || | ||| | || || || || ||||||||||| ||||||||||| |||| |||||| || ||||||||||| ||| ||||| ||
--attctgtgtttatattcgttgtggtatatagtgatacttgtcagtgaaacttggcgcctggaataatccactaaactctacttggaaactctcattgt--agGTATGTGGATGTCATATTGCAACTCATCGAGAAAGCTGGTGATTTTGTAAGTGATGACATTTGGTATCGGGTTGTACAGTTTGTTACCAACGATGAACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacttattgttgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
tactgat putative branch site (score: 2)
tcatccctttt putative PPT
atgtaatatgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaccccatatttcagtacaaaaaattcccttgatatcttgatcagaacttattgttgatgtaatatgtatactgatatcatgtcatcccttttatacagGTATGTTGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
tcacccc
- - - - - - - - - -aaaaaat
- - - - - - - - - - - - - -cccttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - gttgatg