Sequence
atgc intronic sequence ATGC exonic sequence...cctcatttcacttattacactcccatatggtttccaacacttctatgatcatctgcattggtccaattgcttatttcacttttttttctgaaacttgcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
Basic information
species | Glycine max |
transcript | GLYMA07G35240.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G35240.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
cctcatttcacttattacactcccatatggtttccaacacttctatgatcatctgcattggtccaattgcttatttcacttttttttc----tgaaactt--gcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
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----------------gtaatgc-atatg-tttcaagcatagcatagactgttcaagccttttaaaagattgttatggcctgatttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG
upper sequence: GLYMA07G35240.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 4
cctcatttcacttattacactcccatatggtttccaacacttctatgatcatctgcattggtccaattgcttatttcacttttttttctgaaacttgcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
| | | || | ||| | | || | || | || ||| | | || | | | || | | | | ||||| || |||||||| |||||||| ||||| ||||||||||| || || ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||
-gtaagattttgagttgaggttttggatgcctgtgggacgtgcttt--tcttttggcggggttcg-taactgactgtgcgattgactgcgtgg-tggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGACACATTGAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAACTA
upper sequence: GLYMA07G35240.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S67_176V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------cctcatttcacttattacact--cccatatggtttccaacact--------tctatgatcatctgcattggtccaattgcttatttcacttttttttctgaaacttgcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
| || || || | || |||| | | | | || | ||||| || | | | | | ||| | | | || || || |||||| || |||||||| |||||||| || |||||||| || || ||| | || || |||||||||||||| |||||||||||||| |||||||||||| ||
gtaagattgtggtagttgattatgcggtgaagcagatgagagtgattgaaccgtctattggacggggccattgattgatgaagttttcggtagcatgctgaatttgtgcttatctgggtttgcaccggtaataa--tcaggtagtggtatggaa-ttacagGGCATGCCATTTGGCGAAGCAAGCATTTGATGAGGCTATCGCTGAGCTGGATACGTTGAGTGAAGAGTCGTACAAGGACAGCACATTGATCATGCAGTTG
upper sequence: GLYMA07G35240.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S46_127V6.1 (Physcomitrella patens), 3'ss of exon 4
--cctcatttcacttattaca-------ctcccatatggtttc-caacacttctatgatcatctgcattggtccaattgcttatttcacttttttttc--tgaaacttgcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
|||| | | || | || |||||| | | | | | | | |||| |||| || | | | ||| | ||||||| || |||||||| || ||||| || || ||||| ||||| ||||| || || || ||||| ||||| |||||||||||||| ||||||||||||||
gtatgaattttggtcagtagagacttagctgttggttggttttacggcgtgttttttttttcagggattgaatatattggagcttgtgactgaatgccattgactgtggcagGGCATGCCATTTGGCGAAACAAGCATTTGACGAGGCGATTGCTGAGTTGGATACGTTAAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAGCTA
upper sequence: GLYMA07G35240.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S348_15V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------------------cctcatttcacttattacactcccatatggtttccaacacttctatgatcat--ctgcattggtcca-attgcttatttcacttttttttctg-aaacttgcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
| | | | | | | ||| || | | | | |||| || |||||| | |||| | | | | || | || ||| || || |||||||| |||||||| || |||||||| || || ||| | || || ||||| || ||||| |||||||||||||| ||||||||||||||
gtaagagtggctgtgtggcatgcggcgaagcggttgagggtgattgtggaggcgtggatggaacgtgggcgtgggatggatgggtgga-tagcatgtgtgtgggggcg-tggtggattcatggttgtggtggtccgcaatgctgaaacggggtgtggtggtgtgagatttcagAGCATGCCATTTGGCGAAGCAAGCGTTTGATGAGGCGATCGCGGAGCTGGATACGTTGAGCGAGGAGTCGTACAAGGACAGCACGTTGATCATGCAGCTA
upper sequence: GLYMA07G35240.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36243 (Selaginella moellendorffii), 3'ss of exon 4
cctcatttcacttattacactcccatatggtttccaacacttctatgatcatctgcattggtccaattgcttatttcacttttttttctgaaacttgcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
| | | || | ||| | | | ||| || | ||| || | | | |||| ||| ||| || || || | || ||||||||||| || || || || || ||| | ||||| | || ||||| || |||||||||||||||||||||||||||||
---------------------gtgagagcgcctcgtcctctttt-tagttttctccact---tcaactgactttgtggctttgtttcgctgttgcaacagCGCTTGCCAGCTAGCCAAGCAAGCTTTTGACGATGCGATCGCGGAGCTGGACACGCTCAGCGAAGAATCCTACAAGGACAGCACTTTGATCATGCAGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatcatctgcattggtccaattgcttatttcacttttttttctgaaacttgcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
ttatttcacttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctcatttcacttattacactcccatatggtttccaacacttctatgatcatctgcattggtccaattgcttatttcacttttttttctgaaacttgcagGGCCTGTCATTTGGCTAAGCAAGCTTTCGATGAGGCAATTGCAGAGTTAGACACCTTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - -cactccc
- - - - - - - - - - - - - - - - -ccaacac
- - - - - - - - - - - - - - - - - - - - - - - - -catctgc