Sequence
atgc intronic sequence ATGC exonic sequencegtcaatcttcttcttaatgaaatgggaataatgtttatcaactgtcacgaaagaatgaaccatgattcagttgagttctttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGT
Basic information
species | Glycine max |
transcript | GLYMA13G43840.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43840.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 4
--gtcaatcttcttcttaatgaaatgggaataatgtttatcaactgtcacga----aagaatgaacca-tgattcagttgagttctttttt--tcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGT
| | || || || | | |||| || | | || | | |||| | | || | |||| ||| ||| |||||||| |||||||| ||||| || ||||| |||||||||||||||||||| | || ||||||||||||||||| || | |||||||||| | ||
aaagctactatcatcatagaagtactatgtcatcatttagaaaatactatgaccagatgtatgagctaatgtatttaccaagttttttaccaactttcagAGCTTCTGGTGAGCATGAGTCATCAAGGAGGGTGAAGTCTGAACTTCTAGTTCAAATAGACGGTGTAAATAATAGTTCTACCACTGAAGATGGTCAACCA-
upper sequence: GLYMA13G43840.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------gtcaatcttcttcttaatgaaatgggaataatgtttatcaactgt-cacgaaagaatgaaccatgatt--cagttga-------gttctttttttc-----aacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGT
||||| || | | || || |||| | | || ||| || |||| |||| ||| || ||||| | || | ||||||| | ||| || ||||| || ||||| || || |||||||| ||||||||||||||||| || ||||||||||||| ||||| ||||| | |||||||||| | ||
gtatgtgaagtcaagtttgctagttgttcatttactcgagtcaatgaaaatttcttcaatattttgcaccat-aagcatgaatg-tatcattctgctggacaagaaaaaatgtacctatatcgccagttaatgtatttgtccattttttctacatatcagAGCATCTGGTGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGAAGATGGTCAGCCA-
upper sequence: GLYMA13G43840.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 1
---------------------------------------------------------gtcaatcttcttcttaatgaaatgggaataatgtttatcaact-gtcacgaaagaatgaacc---atgattca---gttga---gttctttttttcaa---cagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGT-ACCCGT
||||| || | | || || |||| | | || || | || | | |||| ||| ||| || | || | || | ||| | || ||| || || || || ||||| || || |||||||| ||||||||||||||||| || ||||||||||||| ||||| ||||| | ||| ||||| | ||
gtatgtggagttaattttcctagatgttgctcgtgtctacaagtcaatgaaaaattcctcaatattttgcactat-aagcaagaatg-tatcattctgctagacaacagaaaatgtacctatatgtttaatgtatttatccattttctttcttaatatcagTGCCTCCGGCGAACATGAGTCGTCAAGAAGGGTGAAGTCTGAACTTCTAGTGCAAATTGATGGTGTAAACAATAGCTCCACCACTGATGATGGCCAGCCA-
upper sequence: GLYMA13G43840.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcaatcttcttcttaatgaaatgggaataatgtttatcaactgtcacgaaagaatgaaccatgattcagttgagttctttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGT
|| ||| ||| | | | | | | ||| |||| | ||| || | | ||| || ||| | | | ||||| |||||| |||||||||||||| |||||||| || || ||||| |||||||| || ||||| || | |||| | |||||||||||||||| ||
gtaaattttcct--------gacgatactgagatttcgatactgaaatgaa--aagtatttgtaatt-ggtggaggtgtgat-----gcagGGGTTCTGGAGAGCATGAATCATCAAGAAGGGTGAAATCGGAACTCCTAGTTCAAGTAGATGGAGTGAGCAATACAGCGACAAATGAAGATGGTAGTCGC
upper sequence: GLYMA13G43840.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 4
gtcaatcttcttcttaatgaaatgggaa-taatgtttatcaactgtcacgaa--------agaatgaaccatgattcagtt--gagtt-ctttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGT
||| || | || | ||||| ||| | || | | ||| | | | | || | ||| | || | | | ||| ||||||||| |||||||||||||| |||||| |||| |||||||||||||| |||||||||||||||||||| || ||||| ||| ||||||||||| ||
---aatgttgtggttgagaaaatgtgaacttattgtaagatacttttggtagtttctcttatattggtgttaaactcaaatatgaataacatcgtttgtccagGGCTTCAGGGGAGCATGAATCTTCCAGACGGGTGAAGTCTGAACTTCTGGTTCAGGTTGATGGTGTAAACAACAGTTCTACAGGTGAAGATGGTAGTCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaactgtcacgaaagaatgaaccatgattcagttgagttctttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGT
ttctttttttcaac CT-rich tract
ttcttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaatcttcttcttaatgaaatgggaataatgtttatcaactgtcacgaaagaatgaaccatgattcagttgagttctttttttcaacagGGCTTCTGGGGAGCATGAATCATCCAGAAGGGTCAAGTCTGAACTTCTAGTTCAGGTTGATGGTGTAAATAATAGTTCCACAAATGAAGATGGTACCCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG