Sequence
atgc intronic sequence ATGC exonic sequencegtcatctgaaatctttcaatctgtgtgatattgtatacatcacaattgaatctaatggatagctgcatgattattgaacggttaaatgaatccatagttggaactctggattagcatattgataattgttgtgttgacagATGGAAGGCAAGGTTGGCCAGAGTTTGCACCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC
Basic information
species | Glycine max |
transcript | GLYMA06G18460.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G18460.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G423027_T01 (Zea mays), 3'ss of exon 4
gtcatctgaaatctttcaatctgtgtgatattgtatacatcacaattgaatctaatggatagctgcatgattattgaacggttaaatgaatccatagttggaactctggattagcatattgataattgttgtgttgacagATGGAAGGCAAGGTTGGCCAGAGTTTGCACCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC
| | || | || ||| | | || ||| ||| | || || | || || || || ||| | | ||| || || ||||||| ||| ||||||||||||| | ||||| ||||| ||||| || |||||||| |||||||| | || ||| | | || || || ||| |||||||
-------------------------------ccttagtttggcactctggccttatgtgca--ttcagcattgttggttg-ttctatataccctta------acacttgatgcaccaagagatgtttaaaatggatgcagATGGCAGGGAAGGTTGGCCAGAACTGGCACCCTATGAAGCCATCCATGTTGGAGCTGCAGCACCGCAGATCCCCGAGGCGCTGATCGAGCAGCTGAAGCC
upper sequence: GLYMA06G18460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 3
gtcatctgaaatctttcaatctgtgtgatattgtatacatcacaattgaatctaatggatagctgcatgattattgaacggttaaatgaatccatagttggaactctggattagcatattgataattgttgtgttgacagATGGAAGGCAAGGTTGGCCAGAGTTTGCACCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC
|| | | | | | || | || || ||| || || | | | ||||| || | | |||||| |||||||| ||| | |||||||| || |||||||| |||||||| |||||||||||||| || || || | | | ||||| |||||||||||
------------------------------------------------------gtgagcatcagttcaagtttttgagatttctttggtgtttctgtttttacattg--ctggtttcttgatggttttaa----aatagATGGGAGGCAAGGATGGGCTGAGTTTGCTCCGTATGATGCTATTCACGTCGGAGCAGCAGCACCGGAGATCCCAGAGGCGTTGATTGATCAGTTGAAGCC
upper sequence: GLYMA06G18460.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G50240.1 (Arabidopsis thaliana), 3'ss of exon 3
gtcatctgaaatctttcaatctgtgtgatattgtatacatcacaattgaatctaatggatagctgcatgattatt-gaacggttaaatgaatccatagttggaactctggattagcatattgataattgttgtgttgacagATGGAAGGCAAGGTTGGCCAGAGTTTGCACCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC
| | || | | | |||| | | | | | ||| || | | | || | | || |||||||||| ||||||||| |||||||||||| |||||||| || ||||| |||||||| ||| ||||||| || || || ||| | || ||| | || ||
------------------------------------------------------------------gtaagtactcgctctcccttatgagttccttgcctggcatctt--ttgactcaattgta-----tcttatggcagATGGAAGAAAAGGTTGGCAAGAGTTTGCACCGTATGATGCAATACACGTAGGAGCAGCGGCATCAGAAATCCCTCAGCCCCTTTTGGATCAGCTAAAACC
upper sequence: GLYMA06G18460.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g09690.t01 (Vitis vinifera), 3'ss of exon 3
gtcatctgaaatctttcaatctgtgtgatattgtatacatcacaattgaatctaatggatagctgcatgattattgaacggttaaatgaatccatagttggaactctggattagcatattgataattgttgtgttgacagATGGAAGGCAAGGTTGGCCAGAGTTTGCACCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC
| | || ||| ||| | || | || | | | || ||| | || || |||| | | || ||| | || ||| ||||||||||| ||||||||| |||| |||||| |||||||| |||||||| ||||| |||||||| || || || || ||||||||||| |||||||||||
--------------------------------------aagtcgat-gaaactagagatcttctcagggtataatcatggtgcttatttctccctccttttttctttggaatgcta-atgattaaaattcatggtgatagATGGAAGGCTAGGTTGGCCTGAGTGTGCACCATATGATGCAATTCACGTCGGAGCCGCAGCACCTGAGATACCACAGCCACTTATTGATCAGTTGAAGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaatccatagttggaactctggattagcatattgataattgttgtgttgacagATGGAAGGCAAGGTTGGCCAGAGTTTGCACCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC
tattgat putative branch site (score: 3)
atattgataattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcatctgaaatctttcaatctgtgtgatattgtatacatcacaattgaatctaatggatagctgcatgattattgaacggttaaatgaatccatagttggaactctggattagcatattgataattgttgtgttgacagATGGAAGGCAAGGTTGGCCAGAGTTTGCACCTTATGATGCCATTCACGTTGGAGCAGCAGCACCAGAAATTCCCCAACCACTTATTGACCAGTTGAAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC