Sequence
atgc intronic sequence ATGC exonic sequence...tacttcatgcatctttattttgtatcatgtatgacagtgcatgtcattatatttaggcatagcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACTTGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT
Basic information
species | Glycine max |
transcript | GLYMA08G01800.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os06g36080.1 (Oryza sativa), 3'ss of exon 13
tacttcatgcatctttattttgtatcatgtatgacagtgcatgtcattatatttaggcatagcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACTTGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT-----------------------------------------------------------
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-------------------------------------------------------gatatatgtccatcttgtaatgagacacctttaaac-ctccacaagaaagtgattcct--tatt-tttctttaacttgcgcacacttgggattttgaatgccagCCAACCCAATGGGCTTGCTGTTCCTGATGCAACAATGCATCCTGTCAACTCAAGTTCAGATGTTATTGAACTAATGAGAACAGGACTTGAGAACAGATCT
upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G63640.1 (Arabidopsis thaliana), 3'ss of exon 15
-------------------tacttcatgcatctttattttgtatcatgtatgacagtgcat--------gtcattatatttaggcat-agcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACTTGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT--------------------------------------
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atatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgct-attaggttttactaatgttct-gtggttgcgttcaatacaaaatttccttaacttgcatacATTAGGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAAT
upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 16
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 13
tacttcatgcatctttattttgtatcatgtatgacagtgcatgtcattatatttaggcatagcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACTTGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT-------------------------------------------------------------------------------
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-----------------------gtccta-ataagag-atatccttctctaatctaattaagtatt--tgacatttttattgatatcatttttttt--atgttacaaatattaaat-----ttccttaacttgcatacacttgggatttggaatacttctttaccaaatggcctcgcagTTCCTGATGCAAGCATGCATTCTGTAAGATCAACTGAAGATGTTCTTGAACTGATGAATATTGGGTTGATGAATAGAACTGTTGGCGCCACAACCCTTAA
upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G63640.2 (Arabidopsis thaliana), 3'ss of exon 15
-----------------------------------tacttcatgcatctttattttgtatcatgtatgacagtgcat--------gtcattatatttaggcat-agcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACTTGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT-------------------------------------------
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gtggttccagtcgaagatatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgct-attaggttttactaatgttct-gtggttgcgttcaatacaaaatttccttaacttgcatacattagGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAATATTGG
upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 16
----------tacttcatgcatctttattttgta--tcatgtatgacagtgcatgtcattatatttaggcatagcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACT-TGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT
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aaactactactttttaacttgcttctgtcatgaaatttttttgtaccctttaacttgcacacacttgggatttggagtaccactcaaccaaatggtttagCTGTCCCTGATGCAAGCATGCACC-----CTGTTAAATCAACCGCAGACGTACTGGAATTAATGAATATTGGATTAATGAATAGGGCTGTAGGAGCCACTGCGCT-------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatatttaggcatagcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACTTGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT
cttttacttgtttt CT-rich tract
attcatttactttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacttcatgcatctttattttgtatcatgtatgacagtgcatgtcattatatttaggcatagcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACTTGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - tcatgca
- - - - - - - - - - - - -catgtat
- - - - - - - - - - - - - - - - - - - gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattca