Sequence
atgc intronic sequence ATGC exonic sequencegtctatccatatccctaacattcattcatgtttatatagtaccactcttaatttctcttttaatatgaactgttggttggtgtatccttcggaaacagATATGGTGTTACTGGCGCTGATGATGCTGTGAGAACTTTGAGGTGCATTTGGATTTCTCATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT
Basic information
species | Glycine max |
transcript | GLYMA15G02070.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G02070.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g13150.1 (Oryza sativa), 3'ss of exon 12
gtctatccatatccctaacattcattcatgtttatatagtaccactcttaatttctcttttaatatgaactgttggttggtgtatccttcggaaacagATATGGTGTTACTGGCGCTGATGATGCTGTGAGAACTTTGAGGTGCATTTGGATTTCTCATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT
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-------------gttag--ttcttacatacttctttagg--taattgagaaatgcatgttatttcatatttgtcgtcatgacactttctctttatagGTTTGGTGTAAGTGGTGCTGATGATGCTGTGAAAAGTTTGAAGTGTATTTGGATTTCCCATATTCATGCTGATCACCACACAGGTGTAGCTAGAGTTCTT
upper sequence: GLYMA15G02070.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G379286_T01 (Zea mays), 3'ss of exon 10
gtctatccatatccctaacattcattcatgtttatatagtaccactcttaatttctcttttaatatgaactgttggttggtgtatccttcggaaacagATATGGTGTTACTGGCGCTGATGATGCTGTGAGAACTTTGAGGTGCATTTGGATTTCTCATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT
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----------------gttagttcttgcagatcttctagtaatgca-taaacctatatattaattacatttatgaaagtatactgtcttttgtaacagATTTGGTGTAAATGATGCTGATGAAGCTGTAAAAGGTTTGAGGTGTATTTGGATTTCCCATATTCATGCTGATCACCACACTGGGTTGGCCAGAATTCTT
upper sequence: GLYMA15G02070.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv09s0002g04000.t01 (Vitis vinifera), 3'ss of exon 10
gtctatccatatccctaac-attcattcatgtttatatagtaccact--cttaatttctcttttaatatgaactgttggttggt---gtatccttcggaaacagATATGGTGTTACTGGCGCTGATGATGCTGTGAGAACTTTGAGGTGCATTTGGATTTCTCATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT
| | ||| || || ||| | | | | ||| | ||| |||||| ||| | ||| ||| |||| | | | | ||||||| | |||| || ||||| |||||||||| ||| || || ||||||||||||||||||||||||||||||||| | || |||| || || |||
----gtaaaaatcactgtttatgaatttttaaatgcacaatactgttgttttagtttctccattaccct-aacacttgaatggttttatgtgttctgagaacagATTTAGTGTAGAGGGTGCTGACAATGCTGTGAGGGGTTTAAGATGTATTTGGATTTCTCATATTCATGCTGATCACCATGCGGGTCTGGCAAGAATACTT
upper sequence: GLYMA15G02070.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ19078 (Selaginella moellendorffii), 3'ss of exon 8
gtctatccatatccctaacattcattcatgtttatatagtaccactcttaatttctcttttaatatgaactgttggttggtgtatccttcggaaacagATATGGTGTTACTGGCGCTGATGATGCTGTGAGAACTTTGAGGTGCATTTGGATTTCTCATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT
| | | || || ||| || | ||| || || | ||| |||| || |||| | |||||||| | ||||| ||| | | | | ||| |||||||||||||||||| || ||||||||||| || | || | | | || ||
-----------------gtacttttctatagttttattgttctactacgaacttttttttc--ctaaaact-----------taatcttc----atagATATGGGATCCAAGGCGCCGATTCGGTCCTAGCCAATCTGAAGTGCATTTGGATTTCTCACATCCATGCTGATCATCAGAGCGGACTTACACGCATACTC
upper sequence: GLYMA15G02070.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ13513 (Selaginella moellendorffii), 3'ss of exon 8
gtctatccatatccctaacattcattcatgtttatatagtaccactcttaatttctcttttaatatgaactgttggttggtgtatccttcggaaacagATATGGTGTTACTGGCGCTGATGATGCTGTGAGAACTTTGAGGTGCATTTGGATTTCTCATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT
| | | || || ||| || | ||| | || ||||| || | | || | | |||||||| | ||||| ||| | | | | ||| |||||||||||||||||| || ||||||||||| || | || | | | || ||
-----------------gtacttttctatagttttattgttctactacgtacttttctttccctaaaacttaatgttc----------------atagATATGGGATCCAAGGCGCCGATTCGGTCCTAGCCAATCTGAAGTGCATTTGGATTTCTCACATCCATGCTGATCATCAGAGCGGACTTACACGCATACTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcttaatttctcttttaatatgaactgttggttggtgtatccttcggaaacagATATGGTGTTACTGGCGCTGATGATGCTGTGAGAACTTTGAGGTGCATTTGGATTTCTCATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT
ttttaat putative branch site (score: 3)
tatccttc putative PPT
taatttctcttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctatccatatccctaacattcattcatgtttatatagtaccactcttaatttctcttttaatatgaactgttggttggtgtatccttcggaaacagATATGGTGTTACTGGCGCTGATGATGCTGTGAGAACTTTGAGGTGCATTTGGATTTCTCATATTCATGCTGATCACCATACAGGCTTGGCCAGGATCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT