Sequence
atgc intronic sequence ATGC exonic sequencegtctttatatttctctacttgttgtgaataggtaaaacctatgaattcttgacacaatttcttgcatgtttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
Basic information
species | Glycine max |
transcript | GLYMA04G02020.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g04100.2 (Oryza sativa), 3'ss of exon 5
------------------gtctttatatttctctacttgttgtgaataggtaaaac-ctatgaattcttga-cacaatttcttgcatgtttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
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gggtaccaactatatagaaagtatagattagttaataaatgaccatctagcacaacattgtaaactgtagatcataacatgatttacatt-gtgcaaacagCAATCTTGCAAGAATAGAGAGGAGCGCTGAAAAGCAAGCGAAATCAGGAGCAGAAAATGCTGGGTGGTATGAAAAATG
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G126812_T01 (Zea mays), 3'ss of exon 5
----------gtctttatatttctctacttgttgtgaataggtaaaacctatga--attct-tgacacaatttcttgcatgtttaaatttg-------cagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
||| | | || | | | | || || || ||| || | ||| | | | || ||| || | ||| ||| || | ||||||||||| | ||||| ||||||||||||||||||| | ||||||||||| |||||||| |||||
tgccatatgtgtcagtttcttctttgatgtccttccaa-agttagaacttagaacaattgtacaagggagacactgatatggtttaccttgtccaatacagCAATCTTGCAAGAATAGAGAAGAGTGCTGAAAAACAAGCAAAATCAGGTGCAGAAAATGCTGGGTGGTATGAGAAATG
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G42430.2 (Arabidopsis thaliana), 3'ss of exon 5
-----------------gtctttat-atttctctacttgttgtgaataggtaaaac-ctatgaattcttgaca------caatttcttgcatgtttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
||||| | | | | |||| || || | | || | | | ||| ||| | || | |||||| |||||| ||||||| || ||||| ||||||||||| ||||||||||||||||||||||||||||| ||||| || |||||
gtctatgttataacattccctttaccagatatagcttcgttgccaacagttttcgcgctgctagattcttacagtcctctcattgtcaacttgatcaaattt-cagTAATCTAGCAAGGATTGAAAGGAGTGCACAAAAGCAAGCAAAATCAGGAACTGAAAATGCTGGTTGGTACGAGAAATG
upper sequence: GLYMA04G02020.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g02700.t01 (Vitis vinifera), 3'ss of exon 2
------------------------------------------------------------------gtctttatatttctctacttgttgtgaataggtaaaacctatg--aattcttgacacaat--ttcttgcatgtttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG----------------------
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gtcttgtctttattattgtgtactgcacttaaagataacttctgatttttgcaaacacaactgtaagcacaaattaaagttttatggtttagcatgggcacaatttgtagtaattgtggatactataattaccgaat-tttaaatttgtagTAATCTAGCTAGGATAGAGAGGAGTGCACAAAAACATGCAAAATCTGGCACCGATAATGTTGGGTGGTATGACAAGTGGCAAGGAAATCATTCACTGTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataggtaaaacctatgaattcttgacacaatttcttgcatgtttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
tcttgac putative branch site (score: 3)
atgtttaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctttatatttctctacttgttgtgaataggtaaaacctatgaattcttgacacaatttcttgcatgtttaaatttgcagTAACATAGCAAGAATAGAAAGAAGTGCACAAAAACAAGCAAAATCAGGAACTGAAAATGCTGGATGGTATGAAAAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA