Sequence
atgc intronic sequence ATGC exonic sequencegtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA15G02800.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
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---------------------------------------------------------------------------------------------------------------gtaagttttgatctgaaattattatcttactacc-tgtagttggttaacatcc--tcaccttaaaaagattatgaactctttttagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
upper sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 5
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
| | || | | | | | |||| || || || | | |||| |||| | | || | ||||| || | | ||| || ||||| || ||||||||||||||||| ||||||||||| || || ||||||||||||||||| || || || |||||||||||||| || || | ||
----------------------------------------------------------------------------------gtacgctgaatctgaacctactatcttta-catttttatagatgattcaacatcaccaact---tatgttcca-------------aattttatg-----gtcaatttttcttagGTACGTTGCACCTGAATATGCAATGACTGGCCATCTTCTGGTAAAGAGTGATGTTTACAGCTACGGCGTAGTTCTCCTTGAGCTCCTTACAGGGATGAAA
upper sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
| | | | | | | | | | | ||| ||| | | | | || | | | | || | ||| ||||| || || | |||||||||||||||||||| ||||||||||| || || ||||||||||||||||| || ||||| || |||||||| || || || || ||
-------------------------------------------------------------------------------------------------gtatgctaaatctgaaattactatctttacttcttcatagttgattcaataccatcaactcatattacaaaattctggtca-atttctctt-------agGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA
upper sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g02220.t01 (Vitis vinifera), 3'ss of exon 9
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagctt-cttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
| | || | |||| || | || | | | || ||| || || ||| | | || || | | | ||||||||| ||||||| ||||||| |||||||||||||| ||||||||||| |||||||||||||||||||| ||||| || || || |||||||||||||| |||||||||
---------------------------------------------------------------------------------------------tatattttgcctgtggacggtagtttctttttctcgt---tgtt-ttattgctttgtgcttcaaa-atctcaagtctcttatccaataaacttcttgttttccagCTACTTAGCTCCAGAATATGCAATGACTGGCCATCTTCTCGTGAAAAGTGATGTTTACAGTTATGGTGTAGTCCTTCTTGAGCTCCTAACAGGAAGAAAG
upper sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
| ||| || |||| | ||||| | ||| | ||| | | || | | || | || | ||| | | | |||||| ||| || | ||||| || || || |||||||| |||||||| || ||||| |||||||| |||||||||||||| || ||||| || || || |||||||| ||||| | ||
---------------------------------------------------------------------------------ttctc-ttgtattctcgtttcttctattttttagatatctttggctggac-cgctagcgttgttacttgattcctgcactt---actgat----tga-------tttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA
upper sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S95_115V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
|| || || | || ||| | || | | | || || || || || | ||||| | || ||| | | ||||| ||||| || ||||| || |||||||| || ||||||||||| || || || |||||||| |||||||| ||||| ||||||||||| | ||| | ||
---------------------------------------------------------------------------------------ttcttttacattggaccacatcta--gaactaccacattaat-cagaatgtcaggacttagc-cttggttt---ctgcactgacctattgg--ttgat-tcaaactgcagGTACGTTGCCCCTGAGTACGCAATGACAGGACATCTTCTTGTTAAGAGCGACGTTTACAGTTATGGAGTGGTACTTCTTGAGCTCCTCTCGGGACGGAAA
upper sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S79_45V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattac----catttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
| || |||| || | | || | | ||||| | | |||| | | || | | | |||| | ||||| || ||||| ||||||||||| ||||| ||||| |||||||| || || || || ||||||||||| || || || ||||| || || | || || | |
----------------------------------------------------------------------------------------------------accagtagttatgagtccactttgtagctttacatagtaaaacggaccaagatattttttgcttgtcggaccaaagtgacaa-attgaatcgataatgcagGTATGTAGCACCTGAATATGCGATGACGGGCCACCTTCTTGTAAAGAGCGACGTATACAGCTATGGGGTGGTCCTACTTGAACTTCTTTCGGGGAGGATG
upper sequence: GLYMA15G02800.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S255_47V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
| ||| || | || ||| || || | | | || | || | | | | |||| | ||||| || || ||||||||||| |||||||| || ||| | |||||||| ||||| ||||| || |||||||| ||||| || |||||||| | || | ||
-----------------------------------------------------------------------------------------------tgtttctttgcaccggattacctccaaaatggccatat-ttgtcactattagg-atcgtgccttggtttctgcactgacaaaatattggatctaaactgcagATATGTGGCTCCTGAATACGCAATGACAGGACATTTGCTTGTGAAGAGTGACGTTTATAGTTATGGAGTGGTACTGCTCGAGCTCCTCTCGGGGCGTAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
aactgat putative branch site (score: 3)
ctcttgtttt putative PPT
tgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaatcccttcctagcccttttatgttgatgcttttatggatcatagacgtgatggccaaatgaacacgtttacaaagtactcatttcattccagcttcttgtgtttatcagacttttatgcggatatacattaccatttctgtgcatttcgtctagatgaaactgattttgtgacattgctcttgttttgcagCTACGTAGCTCCTGAATATGCAATGACCGGCCATCTTCTTGTGAAAAGTGATGTTTACAGCTATGGAGTTGTACTCCTTGAGCTCCTAACTGGAAGAAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA