Sequence
atgc intronic sequence ATGC exonic sequence...tctgaatgttccacatatttcatgtttcaacaaggcaacatggtggagattgacccattttaggatgatgaataatgtgctattctgaaattattttcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC
Basic information
species | Glycine max |
transcript | GLYMA04G34140.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G34140.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g30740.1 (Oryza sativa), 3'ss of exon 8
tctgaatgttccacatatttcatgtttcaacaaggcaacatggtggagattgacccattttaggatgatgaataatgtgctattctgaaattattttcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC
| | || | |||| ||| | | | || | | ||||| | ||| | || || || ||| ||| | | |||||||| ||||||||| ||| ||||| ||||||||||| ||||| || |||||||||||||| ||||| ||| | || | ||| ||| | || || || |
---gtaagtcc---atatgtcacttcttgttgtg-taaaacatggaagatttgcttattct--------gattactg----attacaaaaaattctccagGGTTTATGGGTGAACCTTGAGAAGGACCAGTTATTTTGCCTTCTTGGGCCCAATGGAGCTGGTAAAACAACAACAATCAGTTGCTTGACTGGAATCACAC
upper sequence: GLYMA04G34140.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G142249_T01 (Zea mays), 3'ss of exon 8
tctgaatgttccacatatttcatgtttcaacaaggcaacatggtggagattgacccattttaggatgatgaataatgtgctattctgaaattattttcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC
| | | ||| | | | ||| ||| || | || | | | | | |||| | | || ||| || ||| | | ||||||| || ||||||||| ||| ||||| ||| ||||||||||||| || |||||||||||||||||||| || | || | |||| || | || || || |
-gtaagttttcaa------ttagtttttgacataa-aataca-tgcaactatgcttgtcatcatctgattattcat-tgc----ctaaaactttattcagGGCTTATGGGTGAACCTTGAGAAGGACCAGCTATTTTGTCTTCTTGGTCCCAATGGAGCTGGAAAAACAACTACAATCAGTTGTCTGACTGGAATCACAC
upper sequence: GLYMA04G34140.2 (Glycine max), 3'ss of exon 8
lower sequence: AT5G61690.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------tctgaatgttccacatatttcatg--tttcaacaaggcaacatggtggagat----tgacccattttaggatgatgaa---taatgtgctattctgaaattatt--------ttcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC
| ||| || | || | ||| ||| ||| || | ||| | || | ||| | | | || | | | | | | || | ||| |||||||||||||| |||| |||| || |||||||| ||||||||||| ||||| ||||| || || ||||| || |||||| ||||||| | || |||| ||
gtatattatcttccgatggataaatctttccggtaatgaatggtttttgccaaagcttttcctagctgatcatgtaccctgtgttacaacagttacatttattattcaactattaattcattgaaaaaatttcagGGTTTGTGGATGAATATTGCCAAAGATCAGTTGTTTTGTCTTCTTGGACCTAATGGCGCGGGGAAAACAACTACTATTAGTTGTTTGACTGGCATAAATC
upper sequence: GLYMA04G34140.2 (Glycine max), 3'ss of exon 8
lower sequence: AT3G47730.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------------------------------------------------------------------------------tctgaatgttccacatatt-tcatgtttcaacaaggcaacatggtggagattgacccattttag--gatgatgaata-atgtgctattctgaaatt-attt--tcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC
|||||| || || | || || | | | | || ||| | || | ||| ||| || | ||||| | || | || |||| ||||||||||||| |||| |||| || ||||| ||||| |||||||| ||||||||||| || || ||||| || |||| ||||||||| |||| || ||
gtatttcttctaagaaaacaaaagtgaaaaactgatcttcttacgttggttaatttgcaatttcgcatggtagtgtctgttctttaccaaagatgttcaccaaatgataatcttaccattgatctatatctaggacttggatgaaattttactgattatttctccatgtggttttacgtgtttcatttattcagGGTTTGTGGATGAATATTGCCAAAGATCAATTATTCTGTCTTCTTGGACCCAATGGTGCAGGGAAAACAACTACTATCAATTGTTTGACAGGCTTATTTC
upper sequence: GLYMA04G34140.2 (Glycine max), 3'ss of exon 8
lower sequence: AT5G61730.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------tctga--atgttccacatatttcat-gtttcaacaaggcaacatgg-tggagattgacccattttagga-tgatgaataatgtgctattctgaaattatt--------ttcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC
|| || |||| | | | || | | | || | || | ||||| | || | | | | || | | | | | | | | ||| |||||||||||||| |||| |||| || |||||||| ||||||||||| ||||| ||||| || || ||||| || |||||| ||||||| | || |||| ||
gtatgttgctttccgataatgtatggcttttgccaaagatgttcctagctcatgtgacttgagataaaagtgttacaacagttacatttattattcaactattgattcattgaaaaaaattcagGGTTTGTGGATGAATATTGCCAAAGATCAGTTGTTTTGTCTTCTCGGACCTAATGGCGCAGGGAAAACAACTACTATTAGTTGTTTGACTGGCATAAATC
upper sequence: GLYMA04G34140.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv17s0000g05850.t01 (Vitis vinifera), 3'ss of exon 8
---tctgaatgttccacatatttcatgtttcaacaaggcaacatggtggagattgacccattttaggatgatgaataatgtgctattctgaaattattttcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC
| |||| ||| | || |||| | || | ||| | | | | | | | || |||| |||||| ||||||| || |||||||||||| ||||| |||| |||||||||| || |||||||||||||||||||||||||| | |||||||| ||| | || || || |
ccatttgaaaattct-tgtgttaggcaagatgacaaaggggtatatcttattttg-tatgtgtcaatgttgtaaccactgca-tatttgcaaattaccttcagGGATTATGGGTGAACTTTCCAAAGAATCAACTATTTTGTCTCCTTGGACCCAATGGAGCTGGAAAAACTACTACAATTAATTGCTTGACTGGAATTACCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagattgacccattttaggatgatgaataatgtgctattctgaaattattttcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC
gattgac putative branch site (score: 3)
ttattttc putative PPT
tattctgaaattattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgaatgttccacatatttcatgtttcaacaaggcaacatggtggagattgacccattttaggatgatgaataatgtgctattctgaaattattttcagGGTTTGTGGGTGAACTTTGCAAAGGATCAGTTATTTTGTCTTCTAGGACCCAATGGAGCTGGAAAAACTACAGCTATTAATTGTTTGGCAGGGATAACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA