Sequence
atgc intronic sequence ATGC exonic sequencegtatttatctatttttgtttgaaaattatagtcatgatgttgttcttgttctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG
Basic information
species | Glycine max |
transcript | GLYMA09G02960.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 8
--gtattt-atctatttttgtttgaaaattatagtc---atgat--gttgttcttgttctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG
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gtacacttgatatggaactgcaccgggattcttttttaaacaattggttgatggagcattatatacttgtttcctgcagGAGGTTCTTTACTGTGCAAAGAAAGCTGGTGTGACACACATATTGAAAGCTGGAGGAGCTCAG
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 6
---------gtatttatctatttttgtttgaaaatt---atagtcatgatgttgttcttgtt-ctgagca-atgtttt---cctg---cagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG
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gtagtactccgagctgtcttttttccctgggaatatccgatagtacttacatttatcttactgctgagcttatgttttaatcttgtttcagGAGGTTCTGTATTGCGCCAAGAGGGCTGGTGTTACTCACATACTCAAAGCTGGTGGAGCGCAG
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 8
gtatttatctatt--tttgtttgaaaattatag-tcatgatg-------ttgttcttgtt--ctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG
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gtattcttttagtgcctaggatgagacatctatctcattatgaaatcaattattattattatttgattaatgttctcctgtagGAGGTACTCTATTGTGCCAAGAAAGCTGGTGTGACTCATATCCTCAAAGCTGGAGGGGCACAG
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ21362 (Selaginella moellendorffii), 3'ss of exon 5
gtatttatctatttttgtttgaaaattatagtcatgatgttgttcttgttctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG
|| ||||||| | | | | | ||| ||| | |||||| |||||| || | |||||||| ||||| ||||| | |||||||| || ||||||||||||||||||
--------gtacgtttgttt-----tcctcgaaaagttgtcaagcttagTG-GAGCAA---------GCAGGAAGTTTTATATTGTGCTAAGAAAGCTGGAGCTACTCACATCCTAAAAGCTGGAGGAGCACAG
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ21512 (Selaginella moellendorffii), 3'ss of exon 4
gtatttatctatttttgtttgaaaattatagtcatgatgttgttcttgttctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG
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----------------gtacgtgttttattttcctcgaaaagttgtcaagcttagtggag----cacgcagGAAGTTTTATATTGTGCTAAGAAAGCTGGAGCTACTCACATCCTAAAAGCTGGAGGAGCACAG
upper sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ27113 (Selaginella moellendorffii), 3'ss of exon 6
gtatttatctatttttgtttgaaaattatagtcatgatgttgttcttgttctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG
||| | | | |||| | ||||| | ||| ||| | |||||| |||||| || | |||||||| ||||| ||||| | |||||||| || ||||||||||||||||||
gtacgtgttttgttttcctcgaaaagt----------tgtcaagcttagtg-gagcaa---------gcagGAAGTTTTATATTGTGCTAAGAAAGCTGGAGCTACTCACATCCTAAAAGCTGGAGGAGCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgaaaattatagtcatgatgttgttcttgttctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG
tgttttcct CT-rich tract
aaaattatagtcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttatctatttttgtttgaaaattatagtcatgatgttgttcttgttctgagcaatgttttcctgcagGAGGTACTGTATTGTGCAAAGAAGGCTGGGGTGACTCACATTCTCAAAGCTGGAGGAGCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA