Sequence
atgc intronic sequence ATGC exonic sequencegtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatgttggtgtcactcttttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgataacagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
Basic information
species | Glycine max |
transcript | GLYMA17G02720.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G02720.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G069009_T01 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatg-ttggtgtcactcttttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgataacagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
|| ||| | | | || || ||| ||||| || |||| || | || || | || | || |||| ||| || || ||||||||||| ||||||||||||| ||||||||||| || || ||||||||||| || ||| | | || | | |
---------------------------------gtgggtgttctcattgcaatccacgtttctgtttaatctaggatcttgtttgtttatttt--atgaaaaattccatgtttaatg-cagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC
upper sequence: GLYMA17G02720.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatgttggtgtcactcttttcctaaggatgatggaagttttgttctaacttg-aattttcgtgcatgata-acagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
| || |||| | | | | | | || || |||| | |||| || || || |||| | | |||| |||| ||||||||| || ||||| ||| |||| ||||| || |||||||||||| | || |||||||| || |||||| | || || | | |
----------------------------------------gtatgagaattctcctatgattgtgtttctt-ggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
upper sequence: GLYMA17G02720.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatgttggtgtcactct-tttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgata-acagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
| || |||| | | | | | ||| | | | | | | || ||||| | | |||| | |||| ||||||||| || ||||| ||| |||| ||||| || |||||||||||| | || |||||||| || |||||| | || || | | |
----------------------------------------gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
upper sequence: GLYMA17G02720.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G069009_T02 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatg-ttggtgtcactcttttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgataacagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
|| ||| | | | || || ||| ||||| || |||| || | || || | || | || |||| ||| || || ||||||||||| ||||||||||||| ||||||||||| || || |
---------------------------------gtgggtgttctcattgcaatccacgtttctgtttaatctaggatcttgtttgtttatttt--atgaaaaattccatgtttaatg-cagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACAT------------------------------------------
upper sequence: GLYMA17G02720.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G086994_T03 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatgttggtgtcactct-tttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgata-acagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
| || |||| | | | | | ||| | | | | | | || ||||| | | |||| | |||| ||||||||| || ||||| ||| |||| ||||| || |||||||||||| | || |||||||| || |||||| | || || | |
----------------------------------------gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCG-------
upper sequence: GLYMA17G02720.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g01650.t01 (Vitis vinifera), 3'ss of exon 4
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatgttggtgtcactcttttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgataacagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
|||||| | ||| || || || || || | | |||| |||| | ||| | | | | || | || || || | | ||||| ||| |||||||| ||||| |||||||| || |||| ||||||||||||| ||| ||||||||||| ||||||||||| | || | ||| |
gtctgtgtttgttgcaactttttttaatctatcctgttaatgttagatttattggaatcaca--tagcctgaagtttgcag-----ttaagttggctcaaagcttgatatgttgctacagGGTGAAAAAGAGTGCTCCTACTATGTGAAGACAGGACTTTGCAAGTTTGGTGAAACATGTAAATTCCATCATCCACAGCCAGATAGCATACAACTGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgataacagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
ttctaac putative branch site (score: 1)
ttgaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtatcagtttgtgtttattgcgtaaaattatgcgtgctttgggaatgttggtgtcactcttttcctaaggatgatggaagttttgttctaacttgaattttcgtgcatgataacagGCTGAGAAAGAGTGTTCCTATTATGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCACCATCCACAGCCTGCAGGCGTCCAAGCTCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT