Sequence
atgc intronic sequence ATGC exonic sequence...ttgtctcatttctagatattagaaaatgttcacctttgtttttttaagatttagttcatatttgaggcagcttatcattggagtgactgttccaatgtagGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
Basic information
species | Glycine max |
transcript | GLYMA17G06120.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G06120.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g10810.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------------------------ttgtctcatttctagatattagaaaatgttcacct----ttgtttttttaagatttagttcatatttgaggcagcttatcattggagtgactgttccaatgtagGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
| | |||||| || | | | | | || | || | || || | | | |||| || | | ||||||| ||| || || ||| |||||||||||||||| |||||||||||||| |||||||||||||| ||||| | || ||
gtaatttccattttctacttattcataatcaagaaaatggtcactattagactataatatattcaaaatcaatttatttctgaatgcatacatttccttgcatgatccaagcttgtgaacaaataatttctctaacaccagacttacagtttaaacattgataattgcacagGTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG
upper sequence: GLYMA17G06120.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g36800.1 (Oryza sativa), 3'ss of exon 9
ttgtctcatttctagatattagaaaatgttcacctttgtttttttaagatttagttcat-atttgaggcagcttat---cattggagtgactgttccaatgtagGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
|| | || || | |||| | || | | || | | || | | | |||| |||| || || ||| | ||||| ||||| || || ||||| || | |||||||||||||||||||||||||| ||||||||||||||||| || |||||
--gttttggatcagaatggga-aaaacataagttttaccataaccagagttcaacctttcatctcatactgcttccgtgcatttttgttccttttctg-tacagGTTGAATATTCTTGCTGAGCTCCTCTGTTTTGGTGATCGTGAATTCTACAAGGACTGGTGGAATGCCAAAACAGTTGAAGAG
upper sequence: GLYMA17G06120.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G169089_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------ttgtctcatttctagatattagaaaatgttcacctttgtttttttaaga-tttagttcatatttgaggcagc-ttatcattggagtgactgttccaatgtagGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
|| | || ||| || | | || | | || ||| || |||| || || | || | || | | ||| | || || | || || || || | || ||||| ||||||||||| ||||| |||||||||||||||||||| |||||
gttagtatcttgcttcagttcaacagtaccttaaatttgtgcggcagtgattggtttatataacaggttaattgggttttgacctgcatgggactttgatttccattttccatggcattcttgtttgctcttttggttggtttcagGCTGAACATTGTAGCTGAACTCCTCTGTTTCGGTGACCGTGAATTCTATAAGGACTGGTGGAATGCCAAAACTGTTGAAGAG
upper sequence: GLYMA17G06120.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G130749_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------------------------------------------ttgtctcatttctagatattagaaaatgttc----acctttgtttttttaagatttagttcatatttgaggcagcttatcattggagtgactgtt-ccaatgtagGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
|| || | || | || | | || | || ||| || | |||| ||||| | | | | | | | | || |||||||| || || || ||| |||||||||||||||| || ||||||||||| || ||||||||||| || || | || ||
gtagtaaattatattttctatctattcattcaaattcaaatacatgatcgatcctgatattattctaatatcagtcatcgatgcttcttctccgaacat--gcatgctctcggagaaaattatttccttttatgctctttcaaatttgcatatttgcagtttcgaacttatattcatctatacagGTTAAACATACTTGCTGAGATTCTTCGATTTGGTGACCGAGAATTCTACAAAGACTGGTGGAATGCAAAGACAATTGATGAG
upper sequence: GLYMA17G06120.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G19450.1 (Arabidopsis thaliana), 3'ss of exon 9
------------------------------ttgtctcatttctagatattagaaaatgttcacctttgtttt--tttaagatttagttcatatttgaggcagct-tatcattggagtgactg--ttccaatgt---------agGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
| | | ||| | | | |||| | | | | | ||| | |||| | || ||| | | | | ||| ||| |||| | ||| | |||||||| || ||||||||||||| | || || ||||||||||||||||| |||||||||||||| |||| ||| | ||||
gtatgctgtgatcccatctctttcaaaataatttgcaaattcgaaaaaccgaaaaaggctaaatctcatacgaatttgatatttttagtttcttagagtcggtgatgtaatttcagttactgaacgcaaatctcttgtccaaagGTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGAT
upper sequence: GLYMA17G06120.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g01930.t01 (Vitis vinifera), 3'ss of exon 9
ttgtctcatttctagatattagaaaatgttcacctttgtttttttaagatttagttcatatt--tgaggcagcttatcattggagtgactgttccaat---gtagGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
| || ||| ||| || | | || | ||| | | ||||||| | || || | || || || | |||| |||| |||||||||||| || || ||||||||||| ||||| || ||||| ||||| || |||||||||||||| ||||| || || ||
taaaaatataaacagagtttaccaatt-----ctattatctttcatttgtctgaatcatattactaagacatatcatacttagatgcagtgttgcaattatatagGTTAAATATACTTGCTGAGCTTCTTCGTTTTGGGGACCGTGAGTTCTATAAAGATTGGTGGAATGCAAAAACAGTTGAGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagatttagttcatatttgaggcagcttatcattggagtgactgttccaatgtagGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
ctgttcc CT-rich tract
ttcatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtctcatttctagatattagaaaatgttcacctttgtttttttaagatttagttcatatttgaggcagcttatcattggagtgactgttccaatgtagGTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - -acctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcagctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgactg