Sequence
atgc intronic sequence ATGC exonic sequencegtaaggatgtccttgttgctgtataaattaattcctcaggttgcttggaaaccagGGAACTGTTGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAATTAGATCCCAAGTATCACTTCTCTTGTCAATTCATGG
Basic information
species | Glycine max |
transcript | GLYMA11G33240.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G33240.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 9
----------------------------------------------------gtaaggatgtccttgttgctgtataa-attaattcctcaggttgcttggaaaccagGGAACTGTTGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAATTAGATCCCAAGTATCACTTCTCTTGTCAATTCATGG
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gtgaaaccggcttgtcaaatggctgcacgtacggtggttatccctttttaggaccaacgttaccatgatttggtatgacatgaaaaatgcatgat-cttgatgac-agGGAACAATTGCACACGCTCTGGAGAAGACAAAGTACGAGGATTCAGATGTTAAGTGGAGAGAGATGGACCAGAAGTACCATTTCTCTTGCCAATTTACCG
upper sequence: GLYMA11G33240.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G060659_T01 (Zea mays), 3'ss of exon 8
------------------------------gtaaggatg--tccttgttgctgtataaattaattcctcaggttgcttggaaaccagGGAACTGTTGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAATTAGATCCCAAGTATCACTTCTCTTGTCAATTCATGG
| ||| || | ||| || | || | | | || | | ||||| || | || || ||| |||||||||| |||||||||||||||||||| ||||||| ||| | |||| ||||| || ||||| || ||||||| |
gtgaagtgatgggccatcaagtagagtcttgaaagattgattactttttttttgctagtatgacacagaagatgatcttattgacagGGGACAATCGCGCACGCTCTAGAGAAGACAAAGTATGAAGATTCAGATGTGAAGTGGAGAGATCTGGATCAGAAGTACCATTTCTCCTGCCAATTCACTG
upper sequence: GLYMA11G33240.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G045171_T01 (Zea mays), 3'ss of exon 3
----------------------------gtaag--gatgtccttgttgctgtataaattaattcctcaggttgcttgga--aaccagGGAACTGTTGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAATTAGATCCCAAGTATCACTTCTCTTGTCAATTCATGG
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gtgaaggaacaccttctcttctccttgtgccggccggtaccaatcaagtcaaacctgacaaaaaagaaagcaccatcgatgtaacagGGGACGATTGCGCATGCTCTCGAGAAGACAAAGTATGAGGATTCCGATGTCAAGTGGAGGGAAATGGACCACAGGTATCATTTCTCATGCCAGTTTACTG
upper sequence: GLYMA11G33240.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G37180.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------gtaaggatgtccttgttgctgtat--aaattaattcctcaggttgcttggaaa-----ccagGGAACTGTTGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAATTAGATCCCAAGTATCACTTCTCTTGTCAATTCATGG
|| | | || || | | | ||| |||| | || | ||| | ||| |||| |||||||||| || ||||||||||| ||||||||||||||| ||||||||||||| || ||||| || ||||| ||||| | |||||| | ||
gttctttacctttttactttggtaaatttagaccaataaattactcattcttatgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
upper sequence: GLYMA11G33240.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0079g00230.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------gtaaggatgtccttgttgctgtataaattaattcctcaggttgcttggaaaccagGGAACTGTTGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAATTAGATCCCAAGTATCACTTCTCTTGTCAATTCATGG
|| | ||| ||||| | ||| | | ||| ||||| |||||||| |||||||||| ||||||||||||||||| |||||||| |||||||| ||||| |||||||| ||||| ||||| ||||| || ||||| | |
gtgtttttactcattagtggtagatagtttgctactaaatataaactgtcttcttgcta-gctacttactaatctaaaatgccctgaaactagGGAACTATTGCACATGCCTTAGAGAAGACTAAGTACGAAGATTCGGATGTCAAATGGAAGGAATTAGAGCCCAAATATCATTTCTCATGCCAATTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaggatgtccttgttgctgtataaattaattcctcaggttgcttggaaaccagGGAACTGTTGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAATTAGATCCCAAGTATCACTTCTCTTGTCAATTCATGG
aattaat putative branch site (score: 3)
tgtataaattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggatgtccttgttgctgtataaattaattcctcaggttgcttggaaaccagGGAACTGTTGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAATTAGATCCCAAGTATCACTTCTCTTGTCAATTCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA