Sequence
atgc intronic sequence ATGC exonic sequencegtaagaagcaagtaatgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaagTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
Basic information
species | Glycine max |
transcript | GLYMA09G04270.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 10
gtaagaagcaagt-------aatgtaattttgctactaatatt--tgagtcatttgct-tccattcacttaatgaaaatattgttgttggaaagTGGTT---GAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
||| |||| | || | || || || ||| | | || || | | | | | || | | ||| | | || || ||| |||||| || |||| || || ||| | || |||||||||||||| || |||||||| ||||||||||| || || || |||||||| | || ||
gtacattgcaaatctgtttagatttcatctt-cttctatcgctcctatgttgcttatcgtatagttgcctgataagta-attcctatgaaaatgtagTTGTCGAACAAATCTCTGGGAGGGACCACATCCTAAATCATTTAAGCATCCCCGCTGCTTGCTTCACTCATCCAGAGATTAGTATGGTTGGGCTTACAGA
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 10
gtaagaagcaag-taatgtaattttgctactaatatttga-gtcatttgcttccattcactta-atgaaaatattgttgttggaa-agTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
|||| | | | | || | || || | || | | || ||| || | |||| ||| | | | ||| || || ||| ||| ||| || || || | | ||||| ||||||| |||||||||||||||||||| ||||| ||||| |||||||| ||||| ||
gtaaatgttgtgctcacctgtttcttttatccatgctcgatgctgatcactatagttcttatacgagcaaatgttggtctgaatatagTTGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGA
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G152958_T02 (Zea mays), 3'ss of exon 10
gtaagaagcaagtaatgtaattttgctactaatatttgagtcat--ttgct--tccattcacttaatgaaaatattgttgttggaa---agTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
| | | | |||| | | ||| ||| || | | | | | ||| | || | || || ||| ||||||||| || |||||| |||||| | || |||||||||||||| ||||| || |||||||| ||||| || || || |||||||||||||| ||
----gtacttgagagttcctttttcttgtggtttcttggagcatgcttattggtgtacttgtctgatgttgac-ttcctattcaaatgtagTTGTTGAACAAATCTCTGGAAAGGATCACATCCTAAATCATTTAAGCATCCCAGCAGCATGTTTCACCCATCCAGAGATTAGTATGGTTGGATTGACAGA
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------------------gtaagaagcaagtaatgtaattttgctact---aatatttgagtcatttgcttccattca-cttaatgaaaatattgttgttggaaagTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
| | | | | | ||| |||| |||| | || ||| | | ||| | || ||| | || | |||||| |||||| || |||||||| || |||||||| ||||| |||||| | ||||| |||||||||||||| |||||||||||||| || ||||| |||||||| ||
gtaaatggttttatcaatatttcactccaaatgcatctttcttttgtttttccttttctacactgaatacgttag--attgacctttattaaactctatgcatctacttgtgttggctagTGGTGGAGCAAGTCACAGGTAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGTTTTACTCATCCTGAAATAAGTATGGTGGGATTGACAGA
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 10
---------------gtaagaagcaagtaa---tgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaagTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
||| || || | ||| || ||| | | | ||| || | || | | | ||| | | ||| |||||| || ||||||| || |||||||| ||||| |||||| | ||||| ||||||||||| || ||||||||||||||||||||||| ||||| || ||
gtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtattaaactctgagctcttactctgtggctagTGGTCGAGCAAGTCAGCGGCAGAGATCATGTGCTTAATCATCTTAGCATCCCAGCTGCTTGCTTTACTCATCCTGAAATCAGCATGGTGGGATTAACAGA
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 10
----------------------------------------gtaagaagcaagtaatg--taatt-ttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgt-tggaaagTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
| ||| | | || | || ||| | || | | | || ||| | | | | || || || | |||| |||| || || |||| | || || | | || ||| ||| ||||||| ||||||||||| || ||||| ||||||||||| || ||||||||
gtgaatcattctactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacagTGATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTACCAGCGGCTTGTTTCACGCACCCTGAGATCAGCATGGTCGGCTTGACTGA
upper sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------------------------------------------gtaagaagcaagtaatgtaattttgctactaata---tttgagtcattt-gcttccattcacttaatgaa--aatattgttgttggaaagTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
| | | | ||| || | | ||| ||| | |||| || | |||| || ||| || || | ||| |||| || | |||| ||||| | || || |||||| ||| | ||||| ||||||||||| || ||||||||||||||||||||| | |||||
gtatgtcaattggctctaagacaaataaatgaagtatttatttatatatttattgatttttatcctcaatgctccaatgcttcaaagctattcgatggttccacgcaattgataaattttatgatattttagtttgaagtccttaccgagttaatgactttcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTCCAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaagTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
ttaatgaaaatattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaagcaagtaatgtaattttgctactaatatttgagtcatttgcttccattcacttaatgaaaatattgttgttggaaagTGGTTGAACAAGTCACTGGAAGAGATCACGTGCTCAATCATTTAAGCATACCAGCTGCTTGTTTCACTCATCCTGAAATCAGCATGGTTGGATTGACTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT