Sequence
atgc intronic sequence ATGC exonic sequence...ggttttaattgattatattattgtttaataaatttaatttttaacttgctatgccttgtcattgcttttattaacccatgtgtttccctaatcaatgcagTTTAAACTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
Basic information
species | Glycine max |
transcript | GLYMA03G39290.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 3
-ggttttaattgattatattattgtttaataaatttaatttttaacttgctatgccttgtcattgcttttattaacccatgtgtttccctaatcaatgcagTTTAAACTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
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cagctagcaccccctctcgcacggccctgttactgcacattctgttttcgt-tccgttacaatttttattgtgattatgatgccctccccaaaatgtgcagCTTGAATTGGCAGCATCAACATTGTAAGAATCCTCGTCCAAATCCAGATATCAAAACTTTATTCACTGACCATACATGTACTTTACCCAATGGAGCTCCT
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 4
ggttttaattgattatattattgtttaataaatttaatttttaacttgctatgccttgtcattgcttttattaacccatgtgtttccctaatcaatgcagTTTAAACTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
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-gtttgaaagtaatctaatgctgtt-----actttaacggatattctgttt--ccattccaatatttttagtgtgactgatttcccccccaaatgtgcagCTTGAATTGGCAGCATCAGCTTTGTAAGAACCCTCGTCCAAATCCAGATATCAAAACTTTATTCACCGACCATACATGTTCTCCACCCAATGGAGCTCGT
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 4
-------ggttttaattgattatattattgtttaataaatttaatttttaacttgctatgccttgtcattgctt--ttattaacccatgtgtttccctaatcaatgcagTTTAAACTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
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gtgtgtttcttttttctttcctcatgaccattctgtatgttgcagatgaggtttggatgacttcgttgttggatgattcattgtgcatatgttctctt-------gcagCCTCAATTGGCAGCACCAGTTGTGCAAGAATCCTAGGCCAAACCCAGATATTAAAACTCTATTCACAGACCACACTTGCACACTTCCGAATGGTCCTCTC
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 4
ggttttaattgattatattat-tgtttaataaattta-atttttaacttgctatgccttgtcattgcttttattaacccatgtgtttccctaatcaatgcagTTTAAACTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
|||| | || | | | |||| | || | | | || |||| | ||| | | || || ||| | | |||||||||||| ||||| |||||||||||||| ||||| |||||||||| || || ||||| |||||||| ||||| |||||| | ||| | ||||| ||||
-actttacat-atactgctgtgtgttacacgcatacacacactcaaacatatatgacctgttgtatcaaactctagtatgaatgagtccatggtgtatgcagTTTAAATTGGCAGCACCAGCTTTGCAAGAACCCCCGGCCAAATCCAGACATTAAGACATTATTCACAGACCATACATGTGCCCCTTCAAATGGGGCTCTT
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 4
ggttttaattgattatattattgtttaataaatttaatt--tttaacttgctatgccttgtcattgcttttattaacccatgtgtttccctaatcaatgcagTTTAAACTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
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--ttttcaacgtttcatgtgttgttttaaatattcttttcattgtacttaatgagaatttaaataagaattgctttcttgtgcttattttgttaccctgcagTCTCAACTGGCAGCACCAGCTTTGCAAGAACCCAAGGCCGAATCCTGACATCAAGACACTGTTTATTGATCACACTTGTGGACCTCCTAATGGTGCCCGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgctatgccttgtcattgcttttattaacccatgtgtttccctaatcaatgcagTTTAAACTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
attgcttttattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggttttaattgattatattattgtttaataaatttaatttttaacttgctatgccttgtcattgcttttattaacccatgtgtttccctaatcaatgcagTTTAAACTGGCAACACCAGCTTTGCAAAAACCCTAGGCCAAATCCGGATATAAAGACTTTATTCACTGACCACACATGTACACCTCCTAATGGTCCTCTA
- - - - - - - - - - - - - - - - - - - - - - - - ctatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acccatg