Sequence
atgc intronic sequence ATGC exonic sequencegttagcctgtttgtgtctggagtgcttatactcaagcatataaatgaataggtcatattatgaaatcttttgtatgacttttgcatgtgctagataatgatgttccttttatttagcagattatggccttagctttgtttaggagttgtgtgatgatgcgttgtagttgaattttatgaattttccatgatacagGGTGGTGATCAATTATGATTTCCCCACTGGAATTGAGGACTATGTGCACCGTATAGGAAGAACTGGAAGGGCGGGTGCTACTGGAGTGTCATATACCTTT
Basic information
species | Glycine max |
transcript | GLYMA09G03560.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G03560.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g46240.1 (Oryza sativa), 3'ss of exon 6
gttagcctgtttgtgtctggagtgcttatactcaagcatataaatgaataggtcatattatgaaatcttttgtatgacttttgcatgtgctaga-taatgatgttccttttatttagcagattatggc--cttagctttgtttaggagttgtgtgatgatgcgttgtagttgaattttatgaattttccatgatacagGGTGGTGATCAATTATGATTTCCCCACTGGAATTGAGGACTATGTGCACCGTATAGGAAGAACTGGAAGGGCGGGTGCTACTGGAGTGTCATATACCTTT
||| || | | | | || || || | || ||||| | || | | ||| ||| | | || | || | || | | | | | || | | || | ||| || |||||||||||||| || |||||||| || ||||||||||| ||||||||||| | || |||||||| || || |||||||| |||||||| ||
-----------------------------------------------------------gtgaggctttctc----attgtcacaagttaaagtcttctggtgttcgtgttgtctcatcacttacaagtactttacgatattcatattttat-caattgttcaactcactgagacttcacatgtgtttct-----cagAGTAGTGATCAATTATGACTTTCCCACTGGGATCGAGGACTATGTTCACCGTATAGGGCGTACAGGAAGGGCTGGGGCAACTGGAGTCTCATATACTTTC
upper sequence: GLYMA09G03560.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G703415_T02 (Zea mays), 3'ss of exon 7
gttagcctgtttgtgtctggagtgcttatactcaagcatataaatgaataggtcatattatgaaatcttttgtatgacttttgcatgtgctagataatgatgttccttttatttagcagattatggccttagctttgtttaggagttgtgtgatgatgcgttgtagttgaattttatgaattttccatgatacagGGTGGTGATCAATTATGATTTCCCCACTGGAATTGAGGACTATGTGCACCGTATAGGAAGAACTGGAAGGGCGGGTGCTACTGGAGTGTCATATACCTTT
| | | ||| ||| || || | | | || ||| | | | | || | | || || | ||||| || | | || |||| ||||| ||||| ||||||||||| || || ||||| || |||||||||||||| || ||||| | || ||||| || || ||||||||||| || || || |||
-------------------------------------------------------------------------------gtgaggcttatttgattgagatattaattctttaaaacattttaatgtccaaataatacctaaa---tttctgttgctcatttgta-ctgcacaatgtgttttttt-----tacagAGTGGTAATCAATTATGACTTTCCAACTGGGATAGAGGACTATGTGCATCGCATAGGGCGTACAGGAAGAGCTGGCGCTACTGGAGTCTCGTACACATTT
upper sequence: GLYMA09G03560.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0020g00470.t01 (Vitis vinifera), 3'ss of exon 6
gttagcctgtttgtgtctggagtgcttatactcaagcatataaatgaataggtcatattatgaaatcttttgtatgacttttgcatgtgctagataatgatgttccttt-tatttagcagattatggccttagctttgtttaggagttgtgtgatgatgcgttgtagttgaattttatgaattttccatgatacagGGTGGTGATCAATTATGATTTCCCCACTGGAATTGAGGACTATGTGCACCGTATAGGAAGAACTGGAAGGGCGGGTGCTACTGGAGTGTCATATACCTTT
| ||| ||| |||| | | || || || | ||| ||| || ||| ||| | | | | | | | || |||||||| |||||| || ||||| ||||||||||| ||||||||||| || || || ||||| || ||| |||| || ||||| ||||| || ||||| ||||| || |||
---------------------------------------------------------------------------------------------tttatgtagtttctttgcaaatttcacatcattatatatgct---attattgattttgttgggattccctttgtctcattatcttggggtttccatgcctcagGGTCGTAATCAACTATGATTTCCCAACTGGAATTGAAGATTACGTCCACCGAATCGGACGAACCGGGAGGGCTGGTGCAACAGGAGTATCATACACATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggagttgtgtgatgatgcgttgtagttgaattttatgaattttccatgatacagGGTGGTGATCAATTATGATTTCCCCACTGGAATTGAGGACTATGTGCACCGTATAGGAAGAACTGGAAGGGCGGGTGCTACTGGAGTGTCATATACCTTT
ttttccat CT-rich tract
tagttgaattttatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcctgtttgtgtctggagtgcttatactcaagcatataaatgaataggtcatattatgaaatcttttgtatgacttttgcatgtgctagataatgatgttccttttatttagcagattatggccttagctttgtttaggagttgtgtgatgatgcgttgtagttgaattttatgaattttccatgatacagGGTGGTGATCAATTATGATTTCCCCACTGGAATTGAGGACTATGTGCACCGTATAGGAAGAACTGGAAGGGCGGGTGCTACTGGAGTGTCATATACCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG