Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatttccaaactcctatatacagctaagggatgtgctatgcttgatatatactgaatacggtaatccagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCCGATGTT
Basic information
species | Glycine max |
transcript | GLYMA06G23920.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 14
------gtaagcatttccaaactcctatatacagctaagggatgtgctatgcttgatatatactgaatacggta-atccagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCC-GATGTT
| |||||||| | | || || | | | | || || | |||| | | || |||||||| || || || |||||||| ||||| ||||||||||| || ||||| ||||||||| ||||||| |||| || ||||||||||||| | || |
gtaaggctgagcatttctatggttacatggccatc--attttttttttaacctcttaccctctctaataagctgcatgcagGTTGTTGCATCTCAAGACTGGCCAGAAGTTACAAAGTATGCTGGATTGGTGTGTGCTCAGGCTCATCGGCAAGAGCTCATTCAAGATCTTTACAAGACAT-
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 14
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 13
------------------------------gtaagcatttccaaactcctatataca-gctaagggatgtgctatgcttga---tatatactgaatacggtaatc-cagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCCGATGTT
| | ||| || | | || | | | | || | ||| | ||| ||| | ||| | | | |||||||| || || || || ||||| ||||| ||||||||||| || ||||||||||||||| | || || |||| || ||||| || |||| | | |
gtaaggctcattactactttccatttctgcatcaacatgtc-atattcatcaagatatgcacatctttgtcttggttttggacttatctcactcatatgctgctgacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAGGACCTTTACAAAACAT
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 14
-----------------gtaagcatttccaaactcctatat-acagctaa-gggatgtgc-tatgcttgatat-atactgaatacggtaatc----------------cagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCCGATGTT
| |||||| | ||| | ||| | |||| ||| || ||| | | | | ||| || |||||||| || || || || ||||| ||||| ||||||||||| || ||||||||||||||| | || || |||| || |||||||| |||| | | |
gtaaggctcgttactactttgccatttcttcatcaatatgtcacattcatcaggatatgcacatccttatttttgttccgaacttatctgtctgcctctttctgctcacagGTTGTTGCTTCTCAAGATTGGCCAGAAGTTACAAAGTATGCTGGATTGGTTTGTGCTCAGGCACACCGGCAAGAGCTCATTCAAGACCTTTACAAAACAT
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 14
gtaagcatttccaaactcctatatacagctaagggatgtgctatgcttga-tatatactgaatacggtaatccagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCCGATGTT
||||| || | |||| ||| | | | || | ||| |||| | ||| ||| ||| | || ||||| ||||||||||| |||||||| ||||| || |||||||| || ||||| ||||||||| ||||||| ||||||| ||||||||| | | | |
gtaaggatatgaaaacctgtatttcccaaaatctacagttccatgtttgagtccatattgattacaattatacagGTAGTAGCCTCCCAAGACTGGCCAGAAGTCACCAAGTATGCTGGATTGGTATGTGCTCAGGCTCATCGGCAAGAACTTATTCAAGATTTGTATAAAACCT
upper sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------------------------------------------------------------------gtaagcattt---ccaaactcctatataca-gctaagggatgtgctatgcttgatatatactgaatacggtaatccagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCCGATGTT
|| ||| | |||| || | | || |||| || || ||| | | | || ||||| ||||| || ||||| ||||| || || || ||||||||||||||||| |||||||| |||| || | || | ||||| ||||| | | |
gtaagtagctatcttcatgccatttgatcgtatagacatctgttctggatatctgatggctgtatgtttgcagagtcgcgtttgaattatactcttaggtctatacttagggtagtttcctggcaataatagtttttttttg--tatgcagGTGGTAGCTTCGCAGGATTGGCCCGAGGTCACCAAGTATGCAGGGTTGGTGTGTGCTCAAGCTCACCGTCAGGAGTTGATTCAGGATCTGTACAAGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatacagctaagggatgtgctatgcttgatatatactgaatacggtaatccagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCCGATGTT
gcttgat putative branch site (score: 5)
atatatactgaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatttccaaactcctatatacagctaagggatgtgctatgcttgatatatactgaatacggtaatccagGTTGTAGCCTCCCAGGACTGGCCTGAAGTAACAAAGTATGCAGGGTTGGTTTGTGCTCAGCCTCATCGAGAAGAACTAATTCAAGATCTTTTCCGATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC