Sequence
atgc intronic sequence ATGC exonic sequence...gtcatagactacttgaaattgtataagcaaactttagttaagctattttatggggtcttgtactatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG
Basic information
species | Glycine max |
transcript | GLYMA15G42290.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G42290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g15870.3 (Oryza sativa), 3'ss of exon 6
-gtcatagactacttgaaattgta--taagcaaactttagttaagctattttatggggtc--ttgtactatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG
| | | | | | | | || | | ||| | || || | || || |||||| ||| | | ||| | || | |||| || |||||||||||| ||||||||| |||||||| || || ||||| |||||||| || ||||| || |||||||| | ||
acttgtcca-tgttcatagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagt--cgccaacttacttta--cccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG
upper sequence: GLYMA15G42290.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 6
---gtcatagactacttgaaattgtataagc-aaactttagttaagctattttatggggtcttgtactatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG
| || | |||| | || || | | | ||| || | ||| | || | | | || | | |||| || ||| | |||| || |||||||||||| ||| ||||| |||||||| || || ||||| |||||||| || ||||| || |||||||| | ||
cgggacagacgtaacttagtgtatcattagttatattatagatacaatgttt---gcatactagcctttttatcatgcgtaatcgccaacttattttaccc-agGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG
upper sequence: GLYMA15G42290.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G135816_T03 (Zea mays), 3'ss of exon 5
gtcatagactacttgaaattgtataagcaaactttagttaagctattttatggggtcttgta------ctatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG---------------
|| || | | | | || | | | | | |||| | |||| || || | ||||| | | ||| | | ||| ||||| |||| || |||||||||||| |||||| || |||||||| || || ||||| |||||||| |||||||||||||| ||||| | ||
gttttaccgttcctagggcta-atggttggaggtcact---gttattgtgtgggtactaaccaaatatttaccgcatttcatgac-ttgacctccctatgttc-agGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA
upper sequence: GLYMA15G42290.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G135816_T01 (Zea mays), 3'ss of exon 5
gtcatagactacttgaaattgtataagcaaactttagttaagctattttatggggtcttgt------actatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG
|| || | | | | || | | | | | |||| | |||| || || | ||||| | | ||| | | ||| ||||| |||| || |||||||||||| |||||| || |||||||| || || ||||| |||||||| |||||||||||||| ||||| | ||
gttttaccgttcctagggcta-atggttggaggtcact---gttattgtgtgggtactaaccaaatatttaccgcatttcatgac-ttgacctccctatgttc-agGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAG
upper sequence: GLYMA15G42290.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 3'ss of exon 7
gtcatagactact----tgaaattgtataagcaaactttagttaagctattttatggggtcttgtactatcatatttcttaatgttgtctttccttt--gttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG
| | ||| | | ||||||| | | ||| | ||| || | |||||| ||| | ||| | | || | ||| | | | | |||| ||||||||||||||||| |||||||| ||||||||||| |||||||| ||||||||||||||||||||||||||||| ||||
ggccaagatcattgccctgaaatt---cacttcagctt---tcaagtgtccttgtctggtctttgcctaatacgtttttcatatttcttgttcttgttggctgcagGTCAAGAGGAAGAAAGCTTCTCATGCTGGAATGTTTGACATTGCAAAGACCGCAAATAGGCCCATGATACATATTGGTGGCTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatggggtcttgtactatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG
tcttaat putative branch site (score: 3)
ttgtctttcctttgtt CT-rich tract
tatcatatttcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcatagactacttgaaattgtataagcaaactttagttaagctattttatggggtcttgtactatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - ctacttg
- - - - - - - - - - - - - - - - - - - - - - - - tatgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgtac