Sequence
atgc intronic sequence ATGC exonic sequencegtagacagagtcacttgttcatttttaaaactttgaattttactgcttcctcataatgattaatttttatacttcagagtcctgatatatatctatcacttaattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
Basic information
species | Glycine max |
transcript | GLYMA16G30030.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 6
gtagacagagtcacttgttcatttttaaaactttgaattttactgcttcctcataatgattaatttttatacttcagagtcctgatatatatctatcacttaattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
| | ||||| ||| || || || || || ||| ||| | || | || | || | || | | | || | ||||| || ||||| ||||||||||| |||||| ||| ||| || |||||| | ||||| ||||| |||||||| |||
--------------------gtagcaatttctttggttttctctcttttctt----tggtttgtttgtat-cggtggaattatggtgtaattataagtcctgttcatcacaattttgcagGGATATTAAAGGTGCAAATATACTAGTAGATCCTAGTGGTCGTGTTAAGCTTGCAGATTTTGGAATGGCAAAACAT
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 6
gtagacagagtcacttgttcatttttaaaactttgaattttactgcttcctcataatgattaatttttatacttcagagtcctgatatatatctatcacttaattgcatttcttg---taaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
|| || | | ||||| |||| ||| | | | | | | | | || || | ||| | ||| | ||| | || | || | | | |||||||| ||||| ||||| |||||||||||| ||||||| || || ||| | || ||||| || |||||||| |||
---------gtaacat-tccatttc-----cttttgtcgttagttcagcacttcagttccttagatgtaagctaccaagttgtagattat-tttattatttg-tcatgttccataatttgcagGGACATTAAAGGTGCAAACATACTGGTAGATCCTAATGGTCGTGTAAAGCTTGCTGACTTCGGAATGGCAAAACAT
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G093316_T01 (Zea mays), 3'ss of exon 6
gtagacagagtcacttgttcatttttaaaactttgaattttactgcttcctcataatgattaatttttatacttcagagtcctgatatat-atctat-cacttaattgcatttcttgtaaa------gGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
| | || ||| || | | | | || |||| ||| | | || | || ||| | |||| | | || || | | | |||| | ||||||||||| ||||| ||| ||||||| |||||||||| || ||| | || |||||||| |||||||| |||
---------------------gtaacataattttt--ttagattcccttttccggtctattattttatgcatactaggggtttgctattttatcttttcttttgcttactctcttcctaaatttgcagAGACATCAAAGGTGCAAACATATTGGTAGACCCTAATGGCCGTGTAAAGCTTGCTGACTTTGGGATGGCAAAACAT
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 5
gtagacagagtcacttgttcatttttaaaactttgaattttactgcttcctcataatgattaatttttatacttcagagtcctgatatatatctatcacttaattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
| | | |||| | |||| ||| | || | || | | | | | | || | | | | || || | | |||| || ||||||||||| ||||| ||| ||||||| |||||||||| || ||| | || |||||||| |||||||| |||
----gtaacataatttgtatagttttcc--ttttccagcctattattttatgcttactagaggtctgctatttttatttttttttcttttacttactctcttcctaaatttgc-----agAGACATCAAAGGCGCAAACATATTGGTAGACCCTAATGGCCGCGTGAAGCTCGCTGACTTTGGGATGGCAAAACAT
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G175504_T01 (Zea mays), 3'ss of exon 5
gtagacagagtcacttgttcatttttaaaactttgaattttactgcttcctcataatgattaatttttatacttcagagtcctgatatatatctatcacttaattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
||||| | || || || || |||| || || | || | || |||||| || | | | | | |||||| | | ||| | ||||||||||||| || || ||||| ||| || | | |||||| |||||| | ||||||||||| |||||||| |||
gtaga-atttcattttttttgggttcaatcttttgggttgcacattcagcaaatgac-atctatttttgctttt----gcttttgtgtgtg-ctatcaataatttgta-----------gGGACATCAAAGGTGCCAACATACTAGTAAATCCAAGTGGCCGTGTTAAGCTTGCAGACTTTGGAATGGCAAAACAT
upper sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 5
gtagacagagtcacttgttcatt-tttaaaactttgaatttta-ctgcttcctcataatg-----attaatttttatacttcagagtcctgatatatatctatcacttaattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
|| | ||| || || | | || | | |||| | || |||||| | | || |||| || | || |||| | | | | | | || ||||| |||| ||||| || ||||| ||||||||||| ||||| | | ||| || || ||||| ||||| ||||| ||||||||||||
gtgaatcaagttaccaattgttgatccaacaatctgaagtgtagctgctttttattgatttttctattatttgctttatttcaaactttgttcaccttttttctcacaaaccatatttcctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatacttcagagtcctgatatatatctatcacttaattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
catttctt CT-rich tract
atatatatctatcact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagacagagtcacttgttcatttttaaaactttgaattttactgcttcctcataatgattaatttttatacttcagagtcctgatatatatctatcacttaattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG