Sequence
atgc intronic sequence ATGC exonic sequencegtacctgcccttgaatcctcccaaaacttgtttgatgattaagcttgctgtttcttaacaccactgctttctgaccaactgtctagaaatacaattttagttgcatgttgtgtcacttttaaggtatctttattttttttagGTTTCAAACATGCTGCCCTTGCTGAAACGTGGAATAGGAGTACATCACTCTGGTTTACTCCCAATTCTAAAGGAAGTGATTGAGATCTTATTTCAAGAGG
Basic information
species | Glycine max |
transcript | GLYMA08G47700.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g18140.1 (Oryza sativa), 3'ss of exon 5
gtacctgcccttgaatcctcccaaaacttgtttgatgattaagcttgctgtttcttaacaccactgctttctgaccaactgtc-tagaaatacaattttagttgcatgttgtgtcacttttaaggtatctttattttttttagGTTTCAAACATGCTGCCCTTGCTGAAACGTGGAATAGGAGTACATCACTCTGGTTTACTCCCAATTCTAAAGGAAGTGATTGAGATCTTATTTCAAGAGG
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---------------------------------------taattggtccataccttca-accggtgcttgtattttatctttcatttagttcctttgataactgagcgat-tgggataattgagccatgg--ggttttcacagGTTTCAAACATGCTTCCCTTGTTGAAACGTGGCATTGGTGTACATCATTCTGGTCTTTTGCCCATTTTGAAGGAAGTGATTGAGATACTCTTCCAAGAGG
upper sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G040995_T02 (Zea mays), 3'ss of exon 5
gtacctgcccttgaatcctcccaaaacttgtttgatgattaagcttgctgtttcttaacaccactgctttctgaccaactgtctagaaatacaattttagttgcatgttgtgtcacttttaaggtatctttattttttttagGTTTCAAACATGCTGCCCTTGCTGAAACGTGGAATAGGAGTACATCACTCTGGTTTACTCCCAATTCTAAAGGAAGTGATTGAGATCTTATTTCAAGAGG
|| | || || ||| | || | | | | |||| | ||| | || | | | | | | | | || | | | | | |||||||||||||||| ||||| |||||||| || || || || ||||| |||||| | | || ||| |||||||||| |||||||| | ||||| ||||
--------------------------------------ctacgttt-ctatttgt-aatatatgaaccattagcagtactggtaggcaatgctatga-attgataattcatcttaaaactgagccaa-tggagctgtcgcagGTTTCAAACATGCTCCCCTTACTGAAACGCGGCATTGGCGTGCATCATTCTGGTCTGTTGCCTATTTTAAAGGAAGTCATTGAGATACTCTTTCAGGAGG
upper sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0009g01750.t01 (Vitis vinifera), 3'ss of exon 5
gtacctgcccttgaatcctcccaaaacttgtttgatgattaagcttgctgtttcttaacaccactgctttctgaccaactgtctagaaatacaattttagttgcatgttgtgtcacttttaaggtatctttattttttttagGTTTCAAACATGCTGCCCTTGCTGAAACGTGGAATAGGAGTACATCACTCTGGTTTACTCCCAATTCTAAAGGAAGTGATTGAGATCTTATTTCAAGAGG
| ||| | ||| | | | | | | | | | | | || |||||| | |||| || ||| | || || | ||| |||||||||| ||||| ||| | | |||||||||||||| || || || ||||| || || || || || ||||||||||||||||| |||||||||| |
---------------------------gtaaaagattaataatttctttatatatatatattatttatggtgctttagcttattagaaaaattattt------------atggtgcttcca---tactttgaaaatttccagGTTTCAAATATGCTACCCCTCTTAAAACGTGGAATAGGCGTGCACCATTCTGGGTTGCTTCCCATACTGAAGGAAGTGATTGAGATACTATTTCAAGAAG
upper sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S69_14V6.1 (Physcomitrella patens), 3'ss of exon 5
gtacctgcccttgaatcctcccaaaacttgtttgatgattaagcttgctgtttcttaacaccactgctttctgaccaactgtctagaaatacaattttagttgcatgttgtgtcacttttaaggtatctttattttttttagGTTTCAAACATGCTGCCCTTGCTGAAACGTGGAATAGGAGTACATCACTCTGGTTTACTCCCAATTCTAAAGGAAGTGATTGAGATCTTATTTCAAGAGG
|| || ||| | | | | || || | || ||| ||| | || ||| || ||| | | || | ||||||| | | || || || ||||| || ||||| || || ||||||||||| ||||| |||||||| || ||||| |||||||| |||||||||| |
---------------------------------gaagaggaagaagaaaaag----gaaaatggtaggatgtg-ttaagcggctgagaat---gtttctgcaaaattttgaaat-ctgaccaggatcttgcacttaaatcagGTTTCTCATCTACTTCCATTACTGAAGCGCGGAATTGGTGTGCATCACTCTGGCTTACTTCCAATTCTTAAAGAAGTTATTGAGATTCTATTTCAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatacaattttagttgcatgttgtgtcacttttaaggtatctttattttttttagGTTTCAAACATGCTGCCCTTGCTGAAACGTGGAATAGGAGTACATCACTCTGGTTTACTCCCAATTCTAAAGGAAGTGATTGAGATCTTATTTCAAGAGG
tatctttatttttttt CT-rich tract
acttttaaggtatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacctgcccttgaatcctcccaaaacttgtttgatgattaagcttgctgtttcttaacaccactgctttctgaccaactgtctagaaatacaattttagttgcatgttgtgtcacttttaaggtatctttattttttttagGTTTCAAACATGCTGCCCTTGCTGAAACGTGGAATAGGAGTACATCACTCTGGTTTACTCCCAATTCTAAAGGAAGTGATTGAGATCTTATTTCAAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG