Sequence
atgc intronic sequence ATGC exonic sequencegttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttggagtaaatatttgaacttagtgacttacagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
Basic information
species | Glycine max |
transcript | GLYMA08G46710.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G46710.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os08g08000.1 (Oryza sativa), 3'ss of exon 2
gttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttggagtaaatatttgaacttagtgacttacagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
| | || || || || || | ||| | || | | |||||| || | || | || || ||||||||||||| || || ||||||||||||| ||||||||| || |||||||| || | ||||| | | | ||||| |||
-----------------------gtta--ttggctgttaaaataattgatcatttctatcttgctatatcg---tgcagaaataacctaacatttttattatatt--agGCTCTTGTTGTGCTTGTACATGATATGGGTCAAAACTGGGAACTGGTTAGTGACGCACTGAACAGCATTGTTCAATTGAAG
upper sequence: GLYMA08G46710.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G018048_T01 (Zea mays), 3'ss of exon 2
gttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttggagtaaatatttgaacttag---tgacttacagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
|||| | |||| || |||||| || ||| || | | | | || ||| | ||| || ||||| ||||||||||| || ||||||||||||| ||||||||| || |||||||| || ||||||| | | || ||||||
--------------------------------gttctt-ttgggtttgaagttatatatttatttttgagtatgatttgtggtga-tagctaaatatc-ttgaatatttcagGCACTTGTTGTCCTTGTCCATGATATGGGTCAAAACTGGGAACTAGTTAGTGACGCAATCAACAACATCGTGCAGTTCAAG
upper sequence: GLYMA08G46710.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G440943_T01 (Zea mays), 3'ss of exon 15
gttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttggagtaaatatttgaacttagtgacttacagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
||| || || ||| || ||| | || || | | | | || ||| | || | ||||||||||||||||| || |||||||||||| ||||||||| | ||||||||||| | ||||| | || ||||| |||
--------------------------gttactgtctttgcaatattgtgggtcttatttttta-tttgttggca---ataccctaattttctttcatac-------cagGCTCTTGTTGTCCTTGTCCATGATATGGGTGAAAACTGGGAATTGGTTAGTGATGCCCTTAACAGCATCATCCAATTGAAG
upper sequence: GLYMA08G46710.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G475362_T01 (Zea mays), 3'ss of exon 10
gttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttggagtaaatatttgaacttagtgacttacagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
||| || || ||| || ||| || || | || | | | || || ||||||||||||||||| || |||||||||||| ||||||||| | ||||| ||||| | ||||| | || ||||| |||
--------------------------gttactgtctttgcaatattgtgggtcttattttt-----tattggttggcaatacactaatttccttt------cacaccagGCTCTTGTTGTCCTTGTCCATGATATGGGTGAAAACTGGGAATTGGTTAGCGATGCCCTTAACAGCATCATCCAATTGAAG
upper sequence: GLYMA08G46710.1 (Glycine max), 3'ss of exon 18
lower sequence: AT3G24870.1 (Arabidopsis thaliana), 3'ss of exon 15
gttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttgg-agtaaatatttgaacttagtgactt-acagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
|| | ||||| ||| | | || | || || ||| | | | | | | || ||| | | |||| |||||||||||||||||||||||||| || ||||||||||| |||||||||| || ||||| ||| | || | |||
---------------------------gttttttattcgtcatctttcattaacatcgatgtactgttggttgctttatgagtatctaatttattttttcctaccatatagGCGCTTGTTGTCCTGGTGCATGATATGGGGCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
upper sequence: GLYMA08G46710.1 (Glycine max), 3'ss of exon 18
lower sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 14
gttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttgg-agtaaatatttgaacttagtgactt-acagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
|| | ||||| ||| | | || | || || ||| | | | | | | || | | | | |||| |||||||||||||||||||||||||| || ||||||||||| |||||||||| || ||||| ||| | || | |||
---------------------------gttttttattcgtcatctttcattaacatcgatgtactgttggttgctttatgagtatctaatttatctttttctaccatatagGCGCTTGTTGTCCTGGTGCATGATATGGGCCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
upper sequence: GLYMA08G46710.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv07s0005g06680.t01 (Vitis vinifera), 3'ss of exon 15
gttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttggagtaaatatttgaacttagtgacttacagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
||| ||| || ||| | | | ||||| | |||| | | | | ||| || | | | ||| || | |||| | || |||| ||||| ||||| || |||||||||||| |||| ||||||||||| ||||||||||||||||| ||| | |||||||||
-------gttattcttcctttttctttttctga-tgttgtc-ttttttattcttagtgatagaaagtaa--aagtgctgaagttttactagtgttat----tattatagGCACTTGTGGTCCTTGTACATGATATGGGTGCAAATTGGGAGCTTGTAAGTGATGCTATCAACAGCACTCTCCAATTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatttgaacttagtgacttacagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
gacttac putative branch site (score: 2)
ttgttatctattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtctgttgttcgatagttatctcaacttaactcttgtcatgttttggagtaaatatttgaacttagtgacttacagaaagttgttatctattatccaatgttgcagGCTCTTGTTGTCCTGGTGCATGATATGGGTCCAAACTGGGAGCTTGTTAGTGATGCTATCAACAGTACTATACAATTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT