Sequence
atgc intronic sequence ATGC exonic sequencegttggtgtggattactatatcatgtgttgcttctgtcttgagatttgacttcagctgtctagggccacagacaacccaaatccctacccctcccctccaaataacatgcactgtcctttcacttatgtttatatgaattatcagagcatttgttgaagatgcagattttgattcacttcaatattatctcagGTTCCCAGAAGGTTTACCAGTAAGGTTGAGGGAAAGATGGGTTATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAGCCAAGTC
Basic information
species | Glycine max |
transcript | GLYMA19G43790.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 8
gttggtgtggattactatatcatgtgttgcttctgtcttgagatttgacttcagctgtctagggccacagacaacccaaatccctacccctcccctccaaataacatgcactgtcctttcacttatgtttatatgaattatcagagcatttgttgaagatgcagattttgattcacttcaatattatctcagGTTCCCAGAAGGTTTACCAGTAAGGTTGAGGGAAAGATGGGTTATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAGCCAAGTC
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---------------------------------------------------------------------------------------------------gttagtatgttctattctgc-----atacagaactgagatgct---gccttagttgg---cctaaatgttgtttcctat--atgtta-cttagGTCCCAAGAAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGATTTTGTTTACTTTATTTTGTCTGAGGAAGACAAATCATCCGAGCCTAGCC
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 8
gttggtgtggattactatatcatgtgttgcttctgtcttgagatttgacttcagctgtctagggccacagacaacccaaatccctacccctcccctccaaataacatgcactgtcctttcacttatgttta---tatgaattatcagagcatt-tgttgaagatgcagattttgattcacttcaatattatctcagGTTCCCAGAAGGTTTACCAGTAAGGTTGAGGGAAAGATGGGTTATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAGCCAAGTC
|| | | | | | || | | | |||| || | || || | | | || ||| | || | | | | || | || || | || || || | | || |||||||||||||||||||| ||||||||||| ||| | ||||| || || |||||||||||||| ||||
---------------------------------------------------------------------------------------------------gttagtctactcaattttagcatcaaaaccttagccctttattaccaaaatgttgtgctttgtgtccttatattggccc-ttttactgct--tttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGACTTTGTTTACTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTC
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 8
gttggtgtggattactatatcatgtgttgcttctgtcttgagatttgacttcagctgtctagggccacagacaacccaaatccctacccctcccctccaaataacatgcactgtcctttcacttatgtttatatgaattatcagagc-atttgttgaagatgcagattttgattcacttcaatattatctcagGTTCCCAGAAGGTTTACCAGTAAGGTTGAGGGAAAGATGGGTTATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAGCCAAGTC
| || || | |||| |||| |||| | | || | | | || ||| | || | | || | | | | |||| || || | |||||| ||||| || ||||||||||||||||| |||||||||||||||||| || | ||||| || || ||||| || || ||||
-----------------------------------------------------------------------------------------------gttagctactccacatctgcatttc--ttatttttaaaaaacttttttctactagctgccgaatgtct---ttgtcactcggtctact----taatagGTACCGAGGAAGTTTACTAGTAAAACCGAAGGAAAGATGGGTTATGAGGATTTTGTTTACTTCATATTGGCTGAAGAAGACAAGTCATCAGAACCTAGTC
upper sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S34_411V6.1 (Physcomitrella patens), 3'ss of exon 8
gttggtgtggattactatatcatgtgttgcttctgtcttgagatttgacttcagctgtctagggccacagacaacccaaatccctacccctcccctccaaataacatgcactgtcctttcacttatgtttatatgaattatcagagcatttgttgaagatgcagattttgattcacttcaatattatctcagGTTCCCAGAAGGTTTACCAGTAAGGTTGAGGGAAAGATGGGTTATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAGCCAAGTC
|| || || | | ||||| || | ||||| || | || || | | | |||| | || | || | | | | | | ||| ||| || | | || | || ||||||||| | ||| || ||||| || ||| |||||||||||||||||||||| ||||| | || ||||| ||||||||||| ||||| || || || ||
-------------------------------------gtgcatttcgatgtaaaa---ctaggttca---gcttttcaaatttgcactcgatccgatttaacagtgag-agtgtcttctctatagtgctaaagtaacactctaat---tccgttcaaggatttgaatgtaatacgtggtgg----atgtcagGTTCCAAAAAGATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcagagcatttgttgaagatgcagattttgattcacttcaatattatctcagGTTCCCAGAAGGTTTACCAGTAAGGTTGAGGGAAAGATGGGTTATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAGCCAAGTC
ttttgat putative branch site (score: 4)
ttatctc putative PPT
ttcaatattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgtggattactatatcatgtgttgcttctgtcttgagatttgacttcagctgtctagggccacagacaacccaaatccctacccctcccctccaaataacatgcactgtcctttcacttatgtttatatgaattatcagagcatttgttgaagatgcagattttgattcacttcaatattatctcagGTTCCCAGAAGGTTTACCAGTAAGGTTGAGGGAAAGATGGGTTATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAGCCAAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT