Sequence
atgc intronic sequence ATGC exonic sequencegtgagttcacaaccaataacttttattgttaggaataaatcacaaattaatatcctcactttgaaatgcagAAATCTTCTCGTCCTCCTCAAGATAGGACTATGGTAGTTGCCTGCCTTGCTGAAGTTGCTCAGAACATGGGTTTTCCTATTGCAAGCTATGTTGAT
Basic information
species | Glycine max |
transcript | GLYMA08G19960.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G19960.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g15540.1 (Oryza sativa), 3'ss of exon 4
---------------gtgagttcacaaccaataactttta---ttgttaggaataaatcacaaattaatatcctcact--ttgaaatgcagAAATCTTCTCGTCCTCCTCAAGATAGGACTATGGTAGTTGCCTGCCTTGCTGAAGTTGCTCAGAACATGGGTTTTCCTATTGCAAGCTATGTTGAT
||||| | ||| | || | | | || | | | || | || || | | ||||||||||| ||| |||||| ||||||| ||||||||| |||||| | ||||| || |||||| ||||| ||| || | |||||||||
gtgagtaaactctacacatacacacaatctgaaacctatagaagtttctgagttactttagttaacaaatttctttctggtatgagtgcagAAATCTCCTCATCCTCCCCAAGATAAGACTATGGTTGTTGCCACTTTAGCTGAGGTCGCTCAGGGAATGGGAGCTCCAATCTCTGCTTATGTTGAT
upper sequence: GLYMA08G19960.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G408305_T03 (Zea mays), 3'ss of exon 11
------------------------------------------------------------------gtgagttcacaaccaataacttttat-tgttaggaataaatcacaaattaatatcctcactttgaaa-----------------tgcagAAATCTTCTCGTCCTCCTCAAGATAGGACTATGGTAGTTGCCTGCCTTGCTGAAGTTGCTCAGAACATGGGTTTTCCTATTGCAAGCTATGTTGAT
|| | || | | || || ||| | || || | || | | | | ||||||| ||||||||||| | | |||||| ||||||| ||||||||| ||||| | | ||||| ||||||||| | |||||| ||| || | |||||||||
gtatgttaccctcttaccctatctctttgcacatattccatagtcctgtttgctcgacacctattggttaattaattcaataaaagttctatattttttaaacacatggttgtcttgtgttttgcttttgaaactacttcctggaataaatgcagAAATCTCCCCATCCTCCCCAAGATAAGACTATGGTTGTTGCAACCTTAGCTGAGGTTGCTCAGGAAATGGGTGCTCCAATATCTGCTTATGTTGAT
upper sequence: GLYMA08G19960.1 (Glycine max), 3'ss of exon 15
lower sequence: AT4G27640.1 (Arabidopsis thaliana), 3'ss of exon 15
-----------------gtgagttcacaaccaataacttttattgttaggaataaatcacaaattaatatcctcactttgaaatgcagAAATCTTCTCGTCCTCCTCAAGATAGGACTATGGTAGTTGCCTGCCTTGCTGAAGTTGCTCAGAACATGGGTTTTCCTATTGCAAGCTATGTTGAT
| |||| || || ||| | || | | | ||| | | | || ||| || ||||| |||| |||||||| || |||||||| ||||||||||| | |||||||| |||||||| |||||||| |||| || | ||||||||||
gtgggtattagtgaataaagtattcattgaca-tatcttcttccattgaaacttaggcacttactgtt-tcacttcttgtgtctgtagAAAGCTTCACGTCCTCCACAGGATAGGACAATGGTAGTTGCTAGTCTTGCTGAGGTTGCTCAAGACATGGGTCTTCCAATCTCTTCCTATGTTGAT
upper sequence: GLYMA08G19960.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv12s0034g02160.t01 (Vitis vinifera), 3'ss of exon 15
----------------------------gtgagttcacaaccaat---aacttttattgttaggaataaatcacaaattaatatcctcactttgaaatgcagAAATCTTCTCGTCCTCCTCAAGATAGGACTATGGTAGTTGCCTGCCTTGCTGAAGTTGCTCAGAACATGGGTTTTCCTATTGCAAGCTATGTTGAT
||| || ||| | | | ||| || | | | | | | || | | | | | |||||||||| || ||||| || ||||||||||| ||||| ||||| |||||||| || ||||||||| | |||||| ||| |||||| | || ||||||
gtgagttgcaactagttgcctctgatatttgaaatctcaatcctttttgtcatttcatggttgtagtgtgcttgtcactcatttaattattggagagtgcagAAATCCTCACGTCCACCGCAAGATAGGACCATGGTGGTTGCATGCCTTGCAGAGGTTGCTCAGGATATGGGTGCTCCAATTGCAGGATACGTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacttttattgttaggaataaatcacaaattaatatcctcactttgaaatgcagAAATCTTCTCGTCCTCCTCAAGATAGGACTATGGTAGTTGCCTGCCTTGCTGAAGTTGCTCAGAACATGGGTTTTCCTATTGCAAGCTATGTTGAT
tcctcac putative branch site (score: 2)
tcctcacttt CT-rich tract
aataaatcacaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttcacaaccaataacttttattgttaggaataaatcacaaattaatatcctcactttgaaatgcagAAATCTTCTCGTCCTCCTCAAGATAGGACTATGGTAGTTGCCTGCCTTGCTGAAGTTGCTCAGAACATGGGTTTTCCTATTGCAAGCTATGTTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT