Sequence
atgc intronic sequence ATGC exonic sequencegtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattccttttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC
Basic information
species | Glycine max |
transcript | GLYMA01G38580.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattccttttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgca---aataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC
| || | | | | | || || | || || | | | ||||| || || | | | || ||| | ||| | |||| | ||||||| ||||| ||||| ||||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || || ||||||||||| |||||||
----------------------------------------------------------------------------------gtaaaatgggtgttaagttgtttgttgattgcacatatcgatt--ttgttacactgtgtcctg---tttgactgtctggattgttcattaat-tgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattcctt-ttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgca---aataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC
| || || || || || || | || || | | | ||||| || || | | | || ||| | ||| | |||| | ||||||| ||||| ||||| ||||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || || ||||||||||| |||||||
-----------------------------------------------------------------------------------gtaaaatgggtcttaagttgtttgttgattgcacatatcgatt--ttgttacactgtgtcctg---tttgactgtctggattgttcattaat-tgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattcctt--ttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC
| | || || || | ||||| || | | | || || |||| || | | ||| || ||| | | | | | ||| | |||||||| ||||| ||||| |||||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || |||||||| ||||| |||| |
----------------------------------------------------------------------------------------tgtcataccgtgtttgttgatgcatggatcttactatactttgcc-aatttacattc-acttatgtattggttgtttgctaagtgtgtgca---ctt-----ttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattccttttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC
| ||| ||| | |||| || || | | | | | || | | || ||| | || | | |||| ||| || | | | | ||||| ||||| ||||| |||||| ||||||| || ||||| || || || || || ||||||||||| |||||||| || |||||||| ||||| || || |
------------------------------------------------------------------------------------gtaagatgggtcctatgctgtttttattgattttactgtat-tttgttaaattacattt---atttgtcttggttatcgctaatcatttcttgtaccctttgat--gtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G591258_T01 (Zea mays), 3'ss of exon 6
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattccttttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC-----------------
|||| || | | ||| || ||| | | | | | ||| | |||||||| ||||| ||||| |||||| ||||||| || || || ||||| || || || ||||||||||| || ||||| || |||||||| ||||| ||||| |
-----------------------------------------------------------------------------------------------------------------------------------caatttacattc-acttatgtattgattgtttgctaagtgtgtgca---ctt-----ttatgtagactgtggacaatgatcttgcactgaaaatatacataaaggctagGGC-ACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAG
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaat--ccaaattccttttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC
| || ||||| || | ||| |||| |||| ||||||| |||||||||||| || | ||| | | | | || | | |||| || | ||||||| |||||||||||||||||| ||||||| |||||||||||||| ||||| || |||||||||||||| ||||| ||||||||||| || ||||| || |
-------------------------------------------------------------------------------acttggaaaggagtatggtctaatagttttt--------tcatgctctgtt---tgatttgtgttt-----cccttccttttggtctttctgatgttgtaa---ttgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC
aatttttatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattccttttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG