Sequence
atgc intronic sequence ATGC exonic sequencegtaagttgttcttaacaaaaaaaaggcaccaatttcaatattagttctagataacaatcatttacaaacatggattttctgattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
Basic information
species | Glycine max |
transcript | GLYMA20G08140.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 5
gtaagt-----tgttcttaacaaaaaaaaggcaccaatttcaatattagtt--------ctagataaca-----atcatttacaaaca-tggattttctgattcttctacaaatta--cagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
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gtaagtgtgcacactctcttgggggctttggcttttctttgtatccgagttgtgatctgctacatggtataggtgcaatgcttaatcactgcaatgttaaattttgttgcgaaatattcagGCCGACGCGGACGGGAACGGAACCATCGATTACGACGAGTTCATCACAGCGACGATGCACATGAACAGGATGGACAGAGAGGAGCATCTTTACACCGCGT
upper sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g04170.1 (Oryza sativa), 3'ss of exon 3
gtaagttgttcttaacaaaaaaaaggcaccaatttcaatattagttctagataacaatcatttacaaacatggattttctgattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
|| || | || | ||| || || || | | ||||| |||| | | | || ||| | | | | | | ||| || ||||||||||||||||||||||||| || || || || |||||| ||||||| ||| |||||||||||| |||| | ||||||| || |||||||| || |
----gtgagtcct--catagtgaagctacaaactt--agttcagttcgagatgaaatgctaaaactgacaggactcctggaaattcctttcaactttcagGCTGATGCTGATGGCAATGGAATTATCGACTATGAGGAGTTCGTCACCGCGACAGTGCACATGAACAAAATGGATCGAGAAGAGCACCTTTACACGGCAT
upper sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g03970.1 (Oryza sativa), 3'ss of exon 3
gtaagttgttcttaacaaaaaaaaggcaccaatttcaatattagttctagataacaatcatttacaaacatggattttctgattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
|| || | || | ||| || || |||| | | ||||| |||| | | | || ||| | | | | | | ||| || ||||||||||||||||||||||||| || || || || |||||| ||||||| || |||||||||||| |||| | ||||||| || |||||||| || |
----gtgagtcct--catagtgaagctacaaacttcagt-tcagttcgagatgaaatgctaaaactgacaggactcctggaaattcctttcaactttcagGCTGATGCTGATGGCAATGGAATTATCGACTATGAGGAGTTCGTCACCGCGACGGTGCACATGAACAAAATGGATCGAGAAGAGCACCTTTACACGGCAT
upper sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g41270.1 (Oryza sativa), 3'ss of exon 5
-----gtaagttgttcttaacaaaaaaaaggcaccaatttcaatattagttctagataacaatcatttacaaacatggattttctgattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
| || |||| || || | | | || | | | | ||| ||| ||| | | | | || | || ||| |||||||||||| || ||||| || || || |||||||| ||||||||||| || || |||||||||||||| ||| |||| || || || || ||||| || |
gtaaggatagccacgcttaccagaatca---tatggaattgtacttcacattcagaaaactttcagacttacaaaatgtttgtggatttggggggaaaaaaacagGCTGATGCAGACGGCAACGGGACAATCGATTACGAGGAGTTCATCACTGCGACGATGCACATGAACAGGATGGACAGGGAGGAGCACCTCTACACCGCGT
upper sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
lower sequence: AC203294.3_FGT001 (Zea mays), 3'ss of exon 3
-----------------------------gtaagttgttcttaacaaaaaaaag---gcaccaatt--tcaatattagttctagataacaatcatttacaaacatggattttctgattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
| ||| | ||| || | | | | || || | | || | || | | | | || | | | ||| | ||||| || || || || || || || || || ||||| ||||||||||| || || |||||||||||||| ||| |||| |||||||| || ||||| || |
gtgagttttctatgcatgcattcgttctagctcgttttccttgccacacgcgcgcgcggctcgatcgatcggtgctgaagctgcaggaccctgaacgattgatatatgatcgcgaacaaaactaacgcatgcagGCAGACGCGGACGGGAACGGGACGATCGACTACGAGGAGTTCATCACGGCGACGATGCACATGAACAGGATGGACAGGGAAGAACACCTCTACACCGCGT
upper sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G365815_T01 (Zea mays), 3'ss of exon 4
gtaagttgttcttaacaaaa------aaaaggcaccaatttcaatattagttctagataa--caatcatttacaaacatggattttctgattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
|| |||| ||| | | || |||| | |||| || | ||| | || | | | || | |||||| | | || ||| | || |||||||| ||||| ||||| || ||||| |||||||| ||| ||||||||||| |||| ||||||| | || | |||||||| || |||||||| || |
gtgagtt-ttcagagtacaatcttttaaaaaaaaggaattgtgattctt-ttcaaaatgaagaagtaatctgaaaacatccctgctgaaatgctttatacatttccagGCTGACGCTGACGGCAACGGGTTAATTGACTACGACGAATTCGTCACCGCAACAGTGCATATGAACAAACTGGATAGAGAAGAGCACCTTTACACAGCAT
upper sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G167276_T01 (Zea mays), 3'ss of exon 4
gtaagttgttcttaacaaaaaaaaggcaccaatttcaatattagttctagata---acaatcatttacaaacatggattttctgattcttctacaaatta---cagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
| | | || | || || | | | | | | | | | | |||| | ||||| || || || || || || || || || ||||| |||||||||||||| || |||||||||||||| ||| |||| || || || || ||||| || |
---------------------gtgagtttcgttctcgttttttttttcacacgcgcgcggctcggtgctgaagctccaccttaaaaaacccaaaaaatcaacgcagGCGGACGCGGACGGGAACGGCACGATCGACTACGAGGAGTTCATCACCGCGACGATGCACATGAACAGGATGGACAGGGAGGAGCACCTGTACACCGCGT
upper sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagttgttcttaacaaaaaaaaggcaccaatttcaatattagttctagataaca-atcatttacaaa------catggattttctgattctt----ctacaaat-tacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
|| ||| ||||| || | | || | | | | | |||| | | | || ||||| || || || || || ||||||||||||||||||| |||||||| || || || | |||||| ||| | || |||||||| || |||||| | |||||||||||||||||||| | ||||
gtgagtccttcttgtacttgcaagagatttagctttagt-caaatgccgagcaacagagtagggaggggactcaccactaattttgtgtttttttgctctgtgtatctacagGCTGATGCTGATGGTAATGGAACAATAGACTATGGCGAGTTTATCGCAGCCACAATGCATATCAACAGACTTGACAGAGAAGAACATCTTTACTCAGCCT
upper sequence: GLYMA20G08140.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0009g03150.t01 (Vitis vinifera), 3'ss of exon 5
----------------gtaagttgttcttaacaaaaaaaaggcaccaatttca-atattagttctagat---aacaatcatt-tacaaacatggattttctgattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
|| || ||| | || | ||| || || || | ||| | | ||| | || || | ||| | | | ||| | ||| | |||||||||| |||||||||||||||||||| || || ||||| ||||| |||||||||||| ||||||||||| ||| |||||| ||||||||||| ||||
gtaagttctcaccccccaaaaatgatctcagtgaagttcttttgcagattacatgtaaattttttcgatttcagctgtcactctaataattttgatgctttttattttccataaa--aaagGCTGATGCAGATGGCAATGGAACCATTGACTATGATGAGTTTATCACGGCAACAATGCACCTGAACAGAATGGACAAAGAAGACCATCTTTACACAGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctagataacaatcatttacaaacatggattttctgattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
ttctgat putative branch site (score: 3)
ttcttctac CT-rich tract
ataacaatcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttgttcttaacaaaaaaaaggcaccaatttcaatattagttctagataacaatcatttacaaacatggattttctgattcttctacaaattacagGCTGATGCTGATGGCAATGGAACCATTGATTACGACGAGTTCATCACCGCAACAATGCACATGAACAGAATGAACAGAGAAGAACATCTTTACACTGCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC