Sequence
atgc intronic sequence ATGC exonic sequencegtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
Basic information
species | Glycine max |
transcript | GLYMA07G37980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
|| || | || |||||||| || | || | | || || || | | | | | || | ||| | || | ||| |||||| |||| ||||| ||||| ||| |||||||||| || || || ||||| | || ||||||||||||||||| | | || || | |
----------gtgtgaaatctct-cgtaaaatattgctta-ttcatacactt----gtttttcctgttttgaaaa----agagatgttggtacaaataaaat--------------gcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
upper sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G069009_T01 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
| |||| || || | | || || ||| | ||| || |||| || | || || | || | || |||||| | || || |||||||||||| ||||||||||||| ||||||||||| || || |||||||||||||| ||| | | || | | |
-------------------------------gtgggtgttctcattgcaatcca-cgtttctgtttaatctaggatcttgtttgtttattttatga--aaaattccatgtttaatg-cagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACATGTAAATTCCATCACCCAGAACTTGGTTTCCTTACGGAGACGC
upper sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G069009_T02 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
| |||| || || | | || || ||| | ||| || |||| || | || || | || | || |||||| | || || |||||||||||| ||||||||||||| ||||||||||| || || |
-------------------------------gtgggtgttctcattgcaatcca-cgtttctgtttaatctaggatcttgtttgtttattttatga--aaaattccatgtttaatg-cagGGTGAAAAGGAATGTTCCTATTACATGAAAACTGGACATTGCAAGTTTGGAGCTACAT------------------------------------------
upper sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G475017_T03 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
||| | || | | ||| ||| || ||| | ||| || ||| || | | || ||||||| | || ||||| | || || ||||| |||||| ||||||||||||| ||||| ||||| | || |||||||||||||| ||| | | || | ||
-----------------------------------gtgggtgttctca--tttcatgtttctgtttaatctaggatcttgtttatttatttta---tgaaaatttcgtggttaatg-tagGGTGAAAAGGAATGTTCGTATTACATGAAAACTGGACATTGCAAATTTGGAGGTACATGTAAATTCCATCACCCAGAACTTGGTTTTCTTACAGAGACGC
upper sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttc-aaacttgaattttcgtgcatgata-acagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
| || ||||| | | | | | | || || ||| | |||| || || ||| |||| | | |||| |||||| ||||||| || ||||| || |||| ||||| || |||||||||||| | || |||||||| ||||||||| | || || | | ||
----------------------------------------gtatgagaattctcctatgattgtgtttcttg-gattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC
upper sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactct-tttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgata-acagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
| || ||||| | | | | | ||| | | | | | | || ||||| | | |||| | |||||| ||||||| || ||||| || |||| ||||| || |||||||||||| | || |||||||| ||||||||| | || || | | ||
----------------------------------------gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC
upper sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G086994_T03 (Zea mays), 3'ss of exon 4
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactct-tttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgata-acagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
| || ||||| | | | | | ||| | | | | | | || ||||| | | |||| | |||||| ||||||| || ||||| || |||| ||||| || |||||||||||| | || |||||||| ||||||||| | || || | |
----------------------------------------gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCG-------
upper sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g01650.t01 (Vitis vinifera), 3'ss of exon 4
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
|||||| | ||| || | || ||| || | |||| |||| | ||| || | | | |||| ||| || || || | | ||||||| | |||||||| ||||| || ||||| || |||| ||||||||||||| ||| ||||||||||||||||||||||| | || | ||| | |
gtctgtgtttgttgcaactttttttaatctatcctgttaatgttagatttattggaatcaca--tagcct---gaagtttgcagttaagtt--ggctcaaagcttgatatgttgctacagGGTGAAAAAGAGTGCTCCTACTATGTGAAGACAGGACTTTGCAAGTTTGGTGAAACATGTAAATTCCATCATCCACAGCCAGATAGCATACAACTGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
tcctaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG