Sequence
atgc intronic sequence ATGC exonic sequence...cttcctgttttatagaccctattttgttttttaatgttatttcatttttcctttatttttcaccatcagtgattgttttgctatattgattgttatatagGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
Basic information
species | Glycine max |
transcript | GLYMA04G11550.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 10
cttcctgttttatagaccctattttgttttttaatgttatttcatttttcctttatttttcaccatcagtgattgttttgctatattgattgttatatagGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
| | ||| | || || || ||| | || |||| || || ||| | || || | ||||||| |||||||| |||||||||||||| || ||||| |||| || || |||||||| |||| |||||||| || || ||||| ||||| |
--------------------gtcggctcctttgacattcttcaggaattaattt-ctgttgacca-catgatttacattgtca----aatggtctcacagGTTGAGCATCCTGTCACTGAGTGGATAGCTGAAGTAAATTTGCCTGCGGCTCAAGTTGCTGTTGGAATGGGTATACCCCTTTGGCAGATTCCAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 6
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 8
cttcctgttttatagaccctattttgttttttaatgttatttcatttttcctttatttttcaccatcagtgattgttttgctatattgattgttatatagGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
|||| || | | ||||| | | | | | | | | || ||| || || ||||||| ||||| || |||||||||||||| || |||||||||| ||||| |||||||| |||| ||||| || ||||| ||||| ||||| |
-------------------------gtttgctacttgaacatcattgactaataaacctgctgcggaatccttcaaaattttaaatt-atctccatgcagGTTGAGCATCCAGTCACTGAGTGGATAGCTGAAGTAAATCTGCCTGCAGCTCAAGTTGCAGTTGGAATGGGCATACCTCTTTGGCAGATTCCAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G858094_T02 (Zea mays), 3'ss of exon 8
cttcctgttttatagaccctattttgttttttaatgttatttcatttttcctttatttttcaccatcagtgattgttttgctatattgattgttatatagGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
|||| || | | | |||| ||| | | | | | || | | | || | || ||||||| ||||| || || ||||||||||| || |||||||||| ||||| |||||||| |||| ||||| || ||||| ||||| ||||| |
-------------------------gtttgctacttgaactccattgactagttaatatgtaggggaaatcctttacaattttaaattatcttcatgcagGTTGAGCATCCAGTCACCGAGTGGATAGCTGAAGTAAATCTGCCTGCAGCTCAAGTTGCTGTTGGAATGGGCATACCTCTTTGGCAGATTCCAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G377341_T02 (Zea mays), 3'ss of exon 6
cttcctgttttatagaccctattttgttttttaatgttatttcatttttcctttattttt-caccatcagtgattgttttgctatattgattgttatatagGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
||||| || | || || | ||| || |||| ||| | || || || | ||| ||||| | || | | |||| ||||||||||| ||||| |||||||| || ||||| |||||||||| |||||||| | || ||||| || || || | | ||||| |
--gtctgttctaaacttccaatgcagggattt--tgcagagacattcttctatggttcttgcattttgagt-----ttttg----actggcttcctttcagGTAGAACATCCTGTGACTGAATGGATAGCTGAAATAAACTTGCCAGCAGCCCAAGTTGCAGTCGGAATGGGCATACCCCTTTATAACATTCCAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 7
cttcctgttttatagaccctattttgttttttaatgttatttcatttttcctttatttttcaccatcagtgattgttttgctatattgattgttatat---agGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
|| ||| | | | | | || |||| | || ||| | | | || || |||| || ||||||| |||||||| || |||||||| || ||| | ||||| || || || |||||||| |||||||||| || |||||||||||||| ||||
----------------------gtttctttccatacacaccatagctacctttccttttcgaatgaaagattttggtcttgaaaatcgaatgttcgatgtcagGTTGAGCATCCTGTAACCGAGTGGATCGCCGAGGTTAATCTTCCTGCTGCTCAAGTTGCTGTTGGGATGGGAATTCCTCTCTGGCAAATCCCTG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 7
cttcctgttttatagaccctattttgttttttaatgttatttcatttttcctttatttttcaccatcagtgattgttttgctatattgattgttatatagGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
|||| ||| | |||| || || |||| | | || | | | ||| | ||| | || ||| | ||||||| |||||||| ||||||||||| || ||||||||||| || || || |||||||| | |||||||| || |||||||||||||| ||||
--gttggtttcatactgcagctttttgcgttgaaatatattgaaggtccg----gacttgaaaattgaatgacttgtttaacttgatgtttgaggt-cagGTTGAGCATCCTGTCACTGAGTGGATTGCCGAGATAAATCTTCCTGCTGCCCAAGTTGCTGTGGGGATGGGAATTCCTCTCTGGCAAATCCCTG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 7
cttcctgttttatagaccctattttgttttttaatgttatt-tcatttttcctttatttttcaccatcagtgattgttttg-----ctatattgattgttatatagGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
|| || | || | | | ||| | | || || || ||| | ||| || | || || |||| || ||| ||| |||| |||| || || ||||| || |||||||||||||| |||||||||||||||| |||||||| | || ||||| || |||||||||||||||||||
-----tggttctgatacac-gtcatttttatcagtgcaatagccaatttgcacctatgttagatgccatgtaatctttttaaatttcttaattaatttttatcaagGTGGAGCACCCTGTCACGGAGTGGATAGCAGAAGTAAATCTGCCAGCAGCCCAAGTTGCAGTAGGAATGGGGATTCCTCTCTGGCAAATTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcctttatttttcaccatcagtgattgttttgctatattgattgttatatagGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
tattgat putative branch site (score: 3)
tatattgattgttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcctgttttatagaccctattttgttttttaatgttatttcatttttcctttatttttcaccatcagtgattgttttgctatattgattgttatatagGTTGAACATCCTGTTACTGAGTGGATAGCAGAGATAAATCTGCCAGCAGCACAAGTTGCCATTGGGATGGGTATCCCTCTCTGGCAAATTCCTG
- -cctgttt
- - - - - - -agaccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg