Sequence
atgc intronic sequence ATGC exonic sequencegtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
Basic information
species | Glycine max |
transcript | GLYMA15G29860.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g17010.1 (Oryza sativa), 3'ss of exon 4
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtag-aaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
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-------------------------------------------------------------------------------------gtattattccctcctggttctgctattatggcatataata-ttctgtgagaaccaatttatgtacatgtgatatatgctaattaatcttttgttgttcagGTGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGTGTTGGCATCAGTGGTCAAGAAGGACGGCAGGCTGTAATGGCATCAGATTTTGCGATGGG
upper sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g20949.1 (Oryza sativa), 3'ss of exon 4
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacag-attaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
| | | || | || || ||| | | | || || | | |||| | | | ||| | | | |||| |||||| ||||| ||||| ||||| ||||||||| ||||||| |||| ||||||||||| || || |||||||||| ||||| |||||
-----------------------------------------------------------------------------------------gtacagtttttttttctcgccaaatattcaggaattacttgatttactatatttttc---tcaatctgaaaagag-
upper sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G407825_T01 (Zea mays), 3'ss of exon 4
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttat-tatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
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-----------------------------------------------------------------------------------attattccaacttaaaatgtag-gacaaaggaagtagctcagaacttcata-tatgttttatcttcacgagtcaaaaaatatgaaaacatacacgttttcagGTGCAAATGATGTATCCATGATTCAAATGGCTGACGTTGGCATCGGCATCAGTGGGCAAGAGGGAAGGCAAGCTGTTATGGCCTCAGATTTTGCCATGGG
upper sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
| ||| |||| || || ||| | | | | | | |||| ||||| | | | || | |||| | ||| | ||| ||||| | | | ||| ||| | |||| | | | |||||||||||| || |||||||| ||||||||| |||| ||| |||| |||||||| || ||||| || |||||||| ||||| |||||||||||||||||
-----------------------------gtgagtattattcttccaatttat----ttaagactgataacttatgcttgcccaagaccaaaaaattagaag----ggaaaaaaaatctgatc--tgttgtttggttttaggctaacgcttg-------aaatttctattg-gatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
upper sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
| | ||| | || || | ||| | ||| || | || | || ||| || || || ||| | || |||| || || ||| || || ||||| |||||||| ||||||||| ||||||||||||| ||||| || ||||| || || ||||| || ||||| || ||||||||||||||
-------------------------------------------------------------------------------ttcgtgttactagtaagttgaagctct--tcaaaacttcaggttc-tcttacatg-tgtctttagtgcactt-tattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
upper sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ23939 (Selaginella moellendorffii), 3'ss of exon 5
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
|| | |||| || | | ||| | || | |||||| | | | ||||||||||| ||||||||| | ||||| || ||||| | || || ||||| || || ||||| || || |||||||| || ||||| || ||||||||||||
---------------------------------------------------------------------------------------------------------------------gtaatcatctttgtttaggagatctcttgaat-------aatttctctttaatct-ttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
upper sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttt--tctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
| | | |||| | ||| | || | | | ||| |||| ||||||||||| ||||||||| | ||||| || ||||| | || || ||||| || || ||||| || || |||||||| || ||||| || ||||||||||||
-------------------------------------------------------------------------------------------------------------------------------gtaatcatctttgtttaggagttctcttgaataatttctctttaatctttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
ttatgcttttcttt CT-rich tract
tttgtataaaataatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG