Sequence
atgc intronic sequence ATGC exonic sequencegtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
Basic information
species | Glycine max |
transcript | GLYMA11G35460.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 20
gtaattccttcatttttatagaactgtt-ttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
|| || || | | || || || || ||| || ||||| || | | || | || | || || || | ||||||||||||| || ||||| || || ||||| ||||||||||| | ||||||||| |||||||| ||||| ||||| || || ||||| | || ||||||
-------------------------gtagttaactactc--ctgatgttgatatgtgcgaagca-attttgtcct-taacgt-ggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 20
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgcc-atttgta-aaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
| | | || ||||| || ||| | | || ||||| || | | || | || | || || || | ||||||||||||| || ||||| || || ||||| ||||||||||| | ||||||||| |||||||| ||||| ||||| || || ||||| | || ||||||
----------------------------gtagttaacta-cacctgatgttgatatgtgcgaagcaattttgtcct-taacgt-ggcgcaccttaatatcgttctttacattcaacagTGAGGATCCAGATATTCATTTCAAATACATAGAAGCAGCTGCTAGGACTGGACAGATCAAAGAAGTTGAACGTGTAACCAGGGAATCCAACTTTTATGAT
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 6
gtaattccttcatttttatagaactgttttggctggtgggcaa-gtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttc-cccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
| ||| || || | || | ||||| || ||| ||| |||| | ||| | || | | || || || |||| ||||| || || || || || |||||||| |||||||| |||| |||||||||||||||||| ||||| ||||| || ||||| |||| |||||||||
-----------------------gtaatttctcttgttgacagcggaatgcctttctcaaattttgtgt-gtctt-tctcaaaatgcaacacacctgaggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGGACTGGACAAATCAAAGAAGTTGAACGTGTAACCAGAGAGTCAAACTTCTATGAT
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
||| || || | | | || | | || | ||| || | | || | || ||| | ||||| || | || | | | ||||||||||| || || || || || ||||| ||||||||||||| |||||||| |||||||| ||||||||||| || ||||| || | ||||||||||
gtagttactct-tactcctgatgttggtatttctta-----aggtggcatacctta-atattaaatttctcaacatggcatgcattgatattaaattttctttatattc---atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G453474_T01 (Zea mays), 3'ss of exon 4
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttc-cccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT----
| || | | | |||| | | ||||| || ||| ||| |||| | ||| | || | | || || || |||| ||||| || || || || || |||||||| |||||||| |||| ||||||||||||||||| ||||| | ||| || ||||| |||| || ||||||
----------------caggtaatttctcttgctgacagcgga---atgcctttctcaaattttgtgt-gtctt-tctcaaaatgcaacacacctgaggtttctttacatgcaacagcgagGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAGAACTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGATGCTG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
lower sequence: GRMZM2G102756_T01 (Zea mays), 3'ss of exon 4
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttc-cccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
|| | | | |||| | | ||||| || ||| || |||| | ||| | || | | || || || |||| ||||| || || || || || |||||||| |||||||| ||||| | ||||||||||||||| ||||| | ||| || ||||| |||| || ||||||
-------------------gtaatttctcttgctgacagcgga---atgcctttctcaaattatgcgt-gtctt-tctcaaaatgcaacacacctgaggtttctttacatgcaacagCGAGGACCCAGATATCCATTTCAAGTACATAGAAGCAGCAGCAAAAATTGGACAAATCAAAGAAGTTGAACATGTAACCAGAGAGTCAAACTTATATGAT
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccattt--gtaaagggg-atgttgtctgatatcatcagctaatatttttt-tccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
| | | | |||| | ||| ||||| | | | | || | || ||| || ||| | || || || |||||||||||||| || || || |||||||||||||||||||| |||||||| ||||| || |||||||||||||| |||||||| || | |||||||||
---------------------------gtgatatagataaaatctgatctcgtttctgtaaacaagcacgattcttgtatttatatgcttatgtttacaatgtttctctctgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
|||||| ||| | | |||| | ||| | |||| |||| || | | | | | || || | | | | ||||| || || || |||||||||||||| |||||||| |||||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||| || | || ||||||
gtaattttatcaagatcctg---ctgtcattcctg-taaacaag---caccatgcagcaa--------tttgtatttttat-gacttacaatgtcttccctctg----tgtgatagTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 20
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
|||||| || | | |||||| | | || || || ||| | | || | |||| | | |||| ||||| | ||| ||||||||||||||||||||||||| ||||| |||||||| ||||| || ||||||||||| || |||||||||||||||||| ||||||||| |||||||||
gtaatttgtttagtaaggaagaactttgctttctttaggtgcggtacatccaact----------tattttgtgattt-------tcatatcgttttcttttggttcatggaacagTGAGGATCCTGACATTCACTTCAAGTATATTGAAGCTGCTGCTAAAACTGGACAAATTAAGGAGGTTGAGCGTGTGACTCGAGAATCAAACTTCTATGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
ccctaaa putative branch site (score: 3)
agctaatattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattccttcatttttatagaactgttttggctggtgggcaagtgatgccatttgtaaaggggatgttgtctgatatcatcagctaatatttttttccccctaaacttgggacagTGAGGATCCTGACATTCACTTTAAGTACATTGAAGCAGCTGCAAAGACTGGACAAATCAAAGAGGTTGAGCGTGTGACTAGAGAATCAAGTTTCTATGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG