Sequence
atgc intronic sequence ATGC exonic sequence...accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgtatcagatttacattaatgctatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA
Basic information
species | Glycine max |
transcript | GLYMA05G08170.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 19
------accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgtatcagatttacattaatgctatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA
| || |||||| | | || | | | | | | ||| | ||| | | | | | | | ||| | | | | ||| ||||| |||||||| |||||||| || || || || ||||| ||||||||||||||||| || || || || | |||| |||||| | ||||||||
acttggatca-gcaaatattctgtctgtag-tagcgctggaatataattccccaagtttgtcctccatgtactgaaatgactgatgtgtgtgagt----tttccagGGAACAAGTAGGCCAGCTCACTACCACGTCCTTTGGGATGAGAACAATTTCACTGCAGACGAAATGCAGACATTGACAAACAACCTTTGCTACAC----
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 15
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 18
accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgtatcagatttacattaatgctattta-cagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA
|| | || | | |||| | | || | || | | | || | | | | | ||| | | | || | || | | ||||| |||||||| || ||||| || ||||| || ||||| |||||||||||||| || || || || ||| | ||||| |||||| | ||||||||
-ccttttaatcatgtgattgtacagccatggtacttggatcagtagcatgggaatatagtcagattctccgtactgtactgaaatgactgacgtgtggcagGGAACAAGTAGGCCCGCTCACTACCATGTCCTCTGGGATGAGAACAATTTCACAGCAGACGAAATGCAAACACTGACAAACAACCTTTGCTACAC----
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 19
--------------------------------------------------------------------------------------accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgtatcagatttacattaatgctatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA
| | | ||| | || | |||| |||| | | || | ||| | || | | | ||||| | | | | ||| | | | ||||| || || |||| ||||||||||||||||| ||||| |||||||| || || || ||||||||||||||| |||| |||||| | || |||||
gtaccttgttgaactcattaaatattgcaaggcctgaaatttataatagataagaaaaacacagaagttctcaatttctgcaagagaactttcaagttgg-tgttggcatgccaggatggttttgaatg---taaagtactacatgtcaagaatttgt-ttgtactgaaattgacatt--tggcagGGGACCAGCCGACCCGCTCATTATCATGTTCTCTGGGATGAGAACAACTTTACAGCAGATGAGATCCAATCTTTGACGAACAACCTCTGTTACAC----
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 18
accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgta---tcagatttacattaatgctat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA-
||| ||| | | | |||||| | ||| | |||| |||||||| ||||| ||||||||||| ||||| || || |||||||||||||| |||||||| |||| | || || || ||||||| | |||||||||| ||
---------------------------------------------gtaacatgatggcaccctggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 18
accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgta---tcagatttacattaatgctat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA-
||| || | | | |||||| | ||| | |||| |||||||| ||||| ||||||||||| ||||| || || |||||||||||||| |||||||| |||| | || || || ||||||| | |||||||||| ||
---------------------------------------------gtaacttgatggagccctggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ14096 (Selaginella moellendorffii), 3'ss of exon 18
accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgta---tcagatttacattaatgctat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA-
|||| || | | | |||||| | ||| | ||| |||||||| ||||| ||||||||||| ||||| || || |||||||||||||| |||||||| |||| | || || || ||||||| | |||||||||| ||
---------------------------------------------gtaagttgatggagccctggcctttgtagctttgctcatacgacgagattatgttacagGGAACAAGCAGACCAGCTCACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG
upper sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 18
accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgta---tcagatttacattaatgctat-ttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA-
||| || | | | |||||| | ||| | |||| |||||||| ||||| |||||||| || ||||| || || |||||||||||||| |||||||| |||| | || || || ||||||| | |||||||||| ||
---------------------------------------------gtaacttgatggagccctggcctttgtagctttgctcatacgacgagactatgttacagGGAACAAGCAGACCAGCACACTATCACGTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaagatgttaaaagaataatttttgtatcagatttacattaatgctatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA
cattaat putative branch site (score: 3)
ttaaaagaataatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accatacaaatagggtattggtgacttgggatagggtgtaaagaactaagatgttaaaagaataatttttgtatcagatttacattaatgctatttacagGGTACAAGTAGACCAGCTCATTATCATGTTCTGTGGGACGAGAACAATTTCACTGCTGATGAGATCCAATCTCTGACCAACAACTTGTGCTACACGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
-ccataca
- - - - - - - - - tggtgac
- - - - - - - - - - - - - - - - -gggtgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagaa