Sequence
atgc intronic sequence ATGC exonic sequence...tacctggaaaaaaaatgccacattcccttctgtacttcatcttatttagtaaaataaaatatttgaaatgaataatttctaactagtttctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
Basic information
species | Glycine max |
transcript | GLYMA02G39390.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
tacctggaaaaaaaatgccacattcccttctgt-acttcatcttatttagtaaaataaaatatttgaaatgaataatttctaacta--gtttctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
| || | || ||| | | | ||| | ||||| | | | | |||| | | | | | |||| | || | ||||| | ||||||||||| || ||||| | || || ||||| |||||||| || |||||||||||||||||| | || ||||||||||||||||| |||
catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttcaaattacctttgcagt---tcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 6
tacctggaaaaaaaatgccacattcccttctgta-cttcatcttatttagtaaaataaaatattt-gaaatgaataatttctaactagtttctttttctt------agGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
| | | || ||| ||| | || | ||| | || || ||| | ||||| |||| | | | ||||| ||| | | ||| |||| | | |||||||| || || |||| || |||||||| |||||||| || ||||| |||||||||||| | |||| ||| ||||||||||| |||
----tagtataataat----tatttgttattgcatcttaagattcatttgtatcactgcttattttgaaaagcagattttcttcctaaacatgtctacttgcaaacagGTTGGCCTACCAGCTCGTGGTAAAACTTTTACCGCAGCTAAGCTTACAAGGTACCTTCGTTGGTTAGGTCATGAAACCAGACATTTCAATGTTGGAAAG
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
tacctggaaaaaaaatgccacattcccttctgtacttcatcttatttagtaaaataaaatatttgaaatgaataatttctaactagtttctt-tttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
| |||||| | || | | | | || ||| | | || ||| | ||| ||| | | || | | ||||| | | ||||||||||| ||||| | || ||||||||||||||||||||||| ||||||||||||||| | || ||||||||||||||||| |||
-agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
----tacctggaaaaaaaatgccacattcccttctgtacttcatcttatttagtaaaataaaatatttgaaatgaataatttctaactagtttctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
| | || | | | | ||||| || | | | ||| | | | | | || |||||||| || |||| | ||| | |||| |||| | |||||||||||||| || |||| ||||||||||||||||||||||||||||| ||||| |||||| | |||||||||||||||||||| |||
gcaacttccagtaacagcaggtta-attccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttg-taacaaatttatatttc--agGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
tacctggaaaaaaaatgccacattcccttctgtacttcatcttatttagtaaa--ataaaatatttgaa-atgaataatttctaactagtt-tctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
| || || | ||||| | || | ||| || || | | | ||| | || | ||| || |||| || | | | |||| | | || |||||||| ||||||| || |||||||| || || |||||||| | ||| | || ||| |||||||||||||||||||||| |||
----tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagcttcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 7
tacctggaaaaaaaatgccacattcccttctgtacttcatcttatttagtaaaataaaatatttgaaatgaat--aatttctaactagtttctttt--tcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
|| | | ||| ||| | | | ||| | | || | | | || ||| ||| | | | |||| | || || ||||| || ||||| | ||||||||||||||| || |||||| | || |||||||||||| | ||||| |||||||||||||| |||
----tgctttcctagtagtgtattgttgagcgtataatgtgattgtggccaaattcacgctgttaagctacgctgggagttgaatgagtctctgatggtttcagGTTGGGTTACCGGCTCGTGGAAAGACATTCACTGCAGCTAAACTGACCAGATATTTGCGGTGGTTAGGTCATGACACCAAGCACTTCAATGTTGGCAAG
upper sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 7
tacctggaaaaaaaatgccacattcccttctgtacttcatcttatt-tagtaaaataaaatatttgaa---atgaataatttctaactagtttctttttct-tagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
| | || | | | | | || | ||||| | ||| || | || | || ||| | ||| |||| | || |||| | ||||| || || || ||||||| |||||||||||| || || ||||| | |||||| |||||||| ||||||| ||||| ||||| || |||
-atcggggtgcccattattatggt----tggatatattatcttgctgtagccaagttctcaatatcaagctatgttgggagttgaacaagttctagtgactacagGTTGGGTTGCCGGCGCGTGGAAAGACTTTCACTGCAGCTAAGCTGACCCGATATTTGCGATGGCTAGGTCATGATACCAAGCACTTTAATGTCGGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtaaaataaaatatttgaaatgaataatttctaactagtttctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
ttctaac putative branch site (score: 1)
ctagtttctttttctt CT-rich tract
aaaataaaatatttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacctggaaaaaaaatgccacattcccttctgtacttcatcttatttagtaaaataaaatatttgaaatgaataatttctaactagtttctttttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG
- - - -aaaaaaa
- - - - - - - -tgccaca
- - - - - - - - - - - -tcccttc
- - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaatgaa