Sequence
atgc intronic sequence ATGC exonic sequence...tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
Basic information
species | Glycine max |
transcript | GLYMA07G38050.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 12
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtc-aatatctcatcatggtaattaca---cagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
||||| || || ||| | | | | | | ||| |||| | || || || || | | || | | |||||||| || ||||| ||||| ||||| ||||| ||||||||||||||| | |||||| |||| ||||| ||||| ||| | || || |||||||
--------------------gtttgtcaatcttttctttagaatattacgtaacaatcttttg-tattgatatctaagataggatgacgaaaacttaatttcagTATACCATCGAGGAGAAAGTGATTGAGAGGGCATACAAGAAGCTTGCATTGGATGCTTTGGTCATTCAACAAGGCCGACTGGCAGAGCAGAAGA
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 12
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatg----gtaat-tacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
| | | ||| | | || | | | | || | || | | || | |||||| | | ||| | | ||| || | || |||||||| ||||||||||| || ||||| || ||||| ||||||||||| || |||||| |||| || || || || ||||| || || |||||
----gttttatttaatttattttaagatttaaaaacactggtttagcactaagcaat-atcttctatttatttatataacagaatatgcttcatattctatgcagTATACAATTGAGGAAAAGGTGATTGAGAGAGCTTATAAGAAGCTTGCCCTGGATGCTTTGGTCATACAACAGGGTCGATTGGCAGAGCAGAAAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 9
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
| |||| | ||| | || | | | | | |||| ||| || || ||| ||| | | | | || || |||||| || ||||||||||| || ||||| || || || |||||||| ||| | |||||| |||| ||||||||||| ||||| || || ||||| |
-----gtttgtt-gtttctagattaataattactgt--agtgccaa-attttatactt-----ctacctgtatgga-agataatgcaaacaaaattacagTACACTATTGAGGAAAAGGTGATTGAGAGAGCATATAAGAAGCTAGCATTGGATGCTTTGGTTATTCAGCAAGGACGATTGGCAGAGCAGAAAA
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 12
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
| ||||| || | | | |||||| || | || | ||| ||| ||| |||| ||| ||| || | ||||||| ||||||||||| || |||||||||||| | ||||||||||||||||| |||||||||||| |||| || |||||||| |
-----------gttactcttgtac--ccatgtgtatgaagtaagaatgacctggaga--------acttgaactaattctgcat--tggtc-ttatgcagAATGCTATTGAGGCTAAAGTCATTGAGAGAGCTTACAAGAAGTTGGCACTTGATGCTCTGGTTATTCAGCAAGGGAGATTGGCAGAACAGAAAA
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 12
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
||| | ||| | | | | ||| |||| || |||| ||| | ||| | | || | ||||| | | |||||||| ||||| |||||||| |||||||||||| | ||||||||||||||||| ||||| |||||| |||| || |||||||| |
---------gttggtctcctctccg----tgaatttcaagttaaaacagccatgagaggtttaaaattaat-----tatgt----gttgtttgtttacagTCTGCTATTGAGGAGAAAGTGATTGAAAGAGCTTACAAGAAGTTAGCACTTGATGCTCTGGTTATTCAACAAGGGAGATTGGCAGAACAGAAAA
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 12
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
| || | || ||| ||||||| | || || | ||| || | |||||||| ||||| || |||||||||||| | || ||||| ||||||||||| |||||| ||||||| || || || ||| |||| |||||||
----------------------------------gtaaaaggatga--cttgtgtgttatttctttgctgactcgttttct----------gtttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCCGAACAGAGAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 12
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
| || | || ||| ||||||| | || || | ||| || | |||||||| ||||| || |||||||||||| | || ||||| ||||||||||| |||||| ||||||| || || || ||| ||||||||||||
----------------------------------gtaaaaggatga--cttgtgtgttatttctttgctgactcgttttct----------gtttctcagTATACTATTGAAGAGAAAGTCATTGAACGCGCGTACAAAAAGCTTGCACTGGATGCTTTGGTGATCCAACAGGGTCGACTAGCTGAACAGAGAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 12
lower sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 11
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttg-tgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA------
| |||| ||| | || | || ||||| | | | | | |||| || || ||||||||||| |||||| |||||||||| |||||||| | ||||| | || || || ||||| || || || ||| | ||||
------------------------------------------------gtaataagttgattataacttcctttcggcctctcaac-taggagctttgcagTTGACTATCGAGGAAAAAGTTATTGAACGGGCTTACAAAAAGCTTGCCTTGGATGCGTTAGTCATACAACAAGGTCGTTTGGCGGAAGAAAAGAGTATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
tagttatttactattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaagatgtgtttgactctggtttggcagtcattttgaagtgttggtgctttctagttatttactatttgtgtcaatatctcatcatggtaattacacagTATACGATTGAGGAAAAAGTCATTGAAAGGGCTTACAAGAAGCTTGCACTTGATGCTCTGGTGATTCAGCAAGGGCGATTAGCTGAACAGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA