Sequence
atgc intronic sequence ATGC exonic sequence...tcccgtgctcatctatccaggcaccacaatatggtgtggatggctttctaagacctatgagaactaaccaattgtgtttcttttttttttttttaaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
Basic information
species | Glycine max |
transcript | GLYMA13G22790.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G22790.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g07230.1 (Oryza sativa), 3'ss of exon 5
tcccgtgctcatctatccaggcaccacaatatggtgtggatggcttt-ctaagacctatgagaactaaccaattgtgtttctttttttttt------ttttaaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
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-------taaaataataaaaacaaagtaatgtcaaacatcagattatacttctccctctgagaaacaagcatacatgttcaagatctcattaaagtacacttttcagGACACTTGACATCCAAGAGCGATGTATATAGCTTCGGAGTAGTGTTACTCGAGATGTTAACCGGTAGACGATCAATGGACAAGAAGCGGCCTACTGGGGA
upper sequence: GLYMA13G22790.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G007801_T01 (Zea mays), 3'ss of exon 2
tcccgtgctcatctatccaggcaccacaatatg---gtgtg--gatggctttctaagacctatgagaactaaccaattgtgtttcttttttttttttttaaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
|| | | | | || || || || | ||| || | | | ||| | | | |||| || | || | | || |||| ||||||||| |||| ||||||||||||||||| ||||||||| |||| ||||| || || || ||||||||||||||||||||||| || | |||||
-----tgaaaactgaaaaacataacaaaaagtgttagtttaacgattctttctttaagcagttgatatgtcaagttttgttactcatgttatgcatattgttcagGGCACTTGACATCTAAGAGTGATGTTTATAGCTTCGGAGTTGTGCTACTCGAGATGTTGACTGGGAGAAGATCAATGGACAAGAAGCGGCCTACGGGGGA
upper sequence: GLYMA13G22790.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g05720.t01 (Vitis vinifera), 3'ss of exon 5
tcccgtgctcatctatccaggcaccacaatatggtgtggatggctttctaagacctatgagaactaac----caattgtgtttcttttttttttttttaaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
| || | | | || | |||||| || | | || | | | | || | ||| ||| | ||||| ||||||||||||| |||| || |||||||| |||||||| |||||| |||||||||| ||||| || |||||||||||||||||||| ||||| | || ||
----gacatctaagagcaatgctctcaaatatgtgttgttccattcctttgaacttgaaaaatttgacaccttacctgtacaattttggctctttttctcttagGACACTTGACATCTAAGAGCGATGTTTACAGCTTTGGGGTTGTGCTACTTGAGATTTTAACTGGTAGAAGATCAATGGACAAGAAACGCCCTCGCGGAGA
upper sequence: GLYMA13G22790.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ22709 (Selaginella moellendorffii), 3'ss of exon 5
tcccgtgctcatctatccaggcaccacaatatggtgtggatggctttctaagacctatgagaactaaccaattgtgtttcttttttttttttttaaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
| | | | | | | | | ||| || || || | | ||| | ||||| ||||||||||| | || |||||||| |||||||||||||| || || ||||| |||| || ||| |||| ||||||||| | || | ||| ||
--------------------gtaagttcacaaagaaagaaaaaaaattgagagttcttgaacttaaaaggatcgtacctttgtttcct--------ccagGTCACTTGACAGCCAGGAGCGATGTTTACAGCTTTGGAGTTGTCTTCCTGGAGATGCTAACTGGCAGACGATCCATGGACAAGTCTAGACCCACTGGCGA
upper sequence: GLYMA13G22790.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ19239 (Selaginella moellendorffii), 3'ss of exon 5
tcccgtgctcatctatccaggcaccacaatatggtgtggatggctttctaagacctatgagaactaaccaattgtgtttcttttttttttttttaaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
| | | | || | | | | ||| || || || | | ||| | ||||| ||||||||||| | || |||||||| |||||||||||||| || || ||||| |||| || ||| |||| ||||||||| | || | ||| ||
--------------------gtaagttcacaaggaaagaaaaaaacttgagagttcttgaacttaaaaggatcgtacctttgtttcct--------ccagGTCACTTGACAGCCAGGAGCGATGTTTACAGCTTTGGAGTTGTCTTCCTGGAGATGCTAACTGGCAGACGATCCATGGACAAGTCTAGACCCACTGGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctaagacctatgagaactaaccaattgtgtttcttttttttttttttaaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
aactaac putative branch site (score: 1)
ccaattgtgtttcttt CT-rich tract
aattgtgtttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcccgtgctcatctatccaggcaccacaatatggtgtggatggctttctaagacctatgagaactaaccaattgtgtttcttttttttttttttaaccagGACACTTGACAGCTAAAAGTGATGTTTATAGCTTTGGAGTTGTGTTACTTGAGATATTAACAGGAAGAAGATCAATGGACAAGAAGCGCCCGAGTGGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
-cccgtgc
- - - - - - - - - - -caccaca
- - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - -cctatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaacca