Sequence
atgc intronic sequence ATGC exonic sequence...ccacatttgcctacatttttctgcaattttagtactcaacacaaatattacaacaattgcatccacaatttaaaaccatacttttggatgaaaattacagGTTGAGGTATTGAGTTGCATTAGGCATCCAAACATGGTTCTTCTCCTAGGAGCCTGCCCTGAGTACGGCTGCCTTGTATATGAGTACATGTCAAACGGAA
Basic information
species | Glycine max |
transcript | GLYMA17G28970.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G28970.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g12660.1 (Oryza sativa), 3'ss of exon 7
ccacatttgcctacatttttctgcaattttagtactcaacaca---aatattacaacaattgcat--ccacaatttaaaaccatacttttggatgaaaattacagGTTGAGGTATTGAGTTGCATTAGGCATCCAAACATGGTTCTTCTCCTAGGAGCCTGCCCTGAGTACGGCTGCCTTGTATATGAGTACATGTCAAACGGAA
||| | | | | | | || | |||| | | || | | || ||||| | | | | | | || | | ||| | || || | || ||||| ||||||||||||||||| || || || ||||| ||||| |||||||| ||||| || || ||||||||| |||| |
-----tttaaccaaagtcaaaacgactcataatctgaaacagagggagtaattaataaactgcatggtgatgaataagttgtaatttatttattttgttgttcagATAGAAGTGCTTAGCTGCATGAGGCATCCAAACATGGTGCTGCTGCTGGGAGCATGCCCGGAGTACGGGTGCCTGGTGTACGAGTACATGGACTACGGCA
upper sequence: GLYMA17G28970.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G24370.1 (Arabidopsis thaliana), 3'ss of exon 8
ccacatttgcctacatttttctgcaattttagtactcaacacaaatattacaacaattgcatccacaatttaaaaccatacttttggatgaaaattacagGTTGAGGTATTGAGTTGCATTAGGCATCCAAACATGGTTCTTCTCCTAGGAGCCTGCCCTGAGTACGGCTGCCTTGTATATGAGTACATGTCAAACGGAA
| |||| || || | | | | | | || || | | | || |||| | ||||| ||| |||||| ||||||||||| |||||||||||||| ||||||||||| || || || || || || || | ||| || | || || |||| |||| | || || |
------gtaatgacatcttgtaataaagtca-catcagtttctccttattcatttgtttctttctcattttagag------ttttg-----aaaacacagGTCGAGGTATTGAGCTGCATTAGGCATCCGAACATGGTTCTACTTCTTGGGGCTTGTCCGGAATGCGGATGTTTAGTCTACGAGTTCATGGCTAATGGGA
upper sequence: GLYMA17G28970.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g02910.t01 (Vitis vinifera), 3'ss of exon 8
ccacatttgcctacatttttctgcaattttagtactcaacacaaata-ttacaacaattgcatccacaatt--taaaaccatacttttggatgaa---aattacagGTTGAGGTATTGAGTTGCATTAGGCATCCAAACATGGTTCTTCTCCTAGGAGCCTGCCCTGAGTACGGCTGCCTTGTATATGAGTACATGTCAAACGGAA
||| || | || | | | | | ||| | | |||| | || || | || |||| || | || | || | || |||||||| || | || ||||| | ||||| ||||||||||| ||||| ||||||||||| ||||| || ||| | || |||||||||||| | || || |
----attccaagctatgaatttg-attctgaacagcaaactgagcttcttactagaactgt-ttcagaattagcaaggctgtatatatgtttctttctgcttgcagGTTGAAGTTCTCAGCTGCATACGCCATCCTAACATGGTTCTCCTCCTGGGAGCCTGCCCAGAGTATGGATGCTTGGTCTATGAGTACATGGCTAATGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattacaacaattgcatccacaatttaaaaccatacttttggatgaaaattacagGTTGAGGTATTGAGTTGCATTAGGCATCCAAACATGGTTCTTCTCCTAGGAGCCTGCCCTGAGTACGGCTGCCTTGTATATGAGTACATGTCAAACGGAA
aatttaaaaccata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccacatttgcctacatttttctgcaattttagtactcaacacaaatattacaacaattgcatccacaatttaaaaccatacttttggatgaaaattacagGTTGAGGTATTGAGTTGCATTAGGCATCCAAACATGGTTCTTCTCCTAGGAGCCTGCCCTGAGTACGGCTGCCTTGTATATGAGTACATGTCAAACGGAA
ccacatt
- - - -tgcctac
- - - - - - - - - ttctgca
- - - - - - - - - - - - - - - - - ctcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatcca