Sequence
atgc intronic sequence ATGC exonic sequence...agagttgaataatgccagtttaggatggaaccattattttgcaattttgctataaaaactgaaaagactcctagtcctaatgagcccttgtacttggcagTGTTGCAAGATATCAAGAAGCAAATCCTGCAGTTTATACAACTATTATATTCCCATTTCTTTTTGCGGTTATGTTTGGCGACTGGGGTCATGGAATTTGC
Basic information
species | Glycine max |
transcript | GLYMA11G15730.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G15730.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0004g03450.t01 (Vitis vinifera), 3'ss of exon 10
----agagttgaataatgccagtttaggatggaaccattattttgcaattttgctataaaaactgaaaagactcctagtcctaatgagcccttgtacttggcagTGTTGCAAGATATCAAGAAGCAAATCCTGCAGTTTATACAACTATTATATTCCCATTTCTTTTTGCGGTTATGTTTGGCGACTGGGGTCATGGAATTTGC
|| || | || ||| |||| || ||| || | |||| | ||| || || | |||||| | || ||| ||||||||| ||||||||||||||||||||||||||||| || ||||| || || ||||| ||||| || |||||||| || |||||||||||||| |||
tgaaagctttaggataagctgtttttttggtgaacaat---gttgactttattttatacatgtcaaaacga-tcaagatactaatgcaataatttatttgacagTGTTGCTAGATATCAAGAAGCAAATCCTGCAGTTTACACTGTTATTACGTTTCCGTTTCTCTTTGCCGTGATGTTTGGGGATTGGGGTCATGGAATATGC
upper sequence: GLYMA11G15730.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S115_183V6.1 (Physcomitrella patens), 3'ss of exon 11
---------------------------------------------------------------------------------------------agagttgaataatgccagtttaggatggaaccattattttgcaattttgctat--aaaaactgaaaagactcctagtcctaatgagcccttgtacttggcagTGTTGCAAGATATCAAGAAGCAAATCCTGCAGTTTATACAACTATTATATTCCCATTTCTTTTTGCGGTTATGTTTGGCGACTGGGGTCATGGAATTTGC-
| || | | | || ||| || || | | | | | ||||| | || || | | | ||| |||| | || || ||||| ||||||||||| || |||| | | || | ||| ||||||||| || |||||||||||||||||||||||||| ||||| || ||
gtaagtttcaacaaaacatgtcgatggaaataggaattccaagaaatctagagtaggcatttttcgatcgaatacaaacgacatacactgtgaatcttttcaaagatcgaggcagagatcaaagcagagtctaaggaccagcatgttcaaaaattctgaacacattatttacataccagcttttgt-----gtagGGTGGCAAGGTATCAAGAAGCGAACCCTGGATGCTTCACGATCGTTACATTCCCATTCCTCTTTGCGGTTATGTTTGGCGACTGGGGACATGGCATA-GCA
upper sequence: GLYMA11G15730.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ10256 (Selaginella moellendorffii), 3'ss of exon 9
agagttgaataatgccagtttaggatggaaccattattttgcaattttgctataaaaactgaaaagactcctagtcctaatgagcccttgtacttggcagTGTTGCAAGATATCAAGAAGCAAATCCTGCAGTTTATACAACTATTATATTCCCATTTCTTTTTGCGGTTATGTTTGGCGACTGGGGTCATGGAATTTGC
| || ||| | || | | | || || ||| | ||| || |||||||| |||||||||||||||||| || | ||||| || | | | ||| |||||||| || ||||| |||||||| ||||||||||| |||||| |
----------------------------------------gtaagcttg---tgaaccattattgg----ctgagtcttatggtcttttggtctc--cagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGAGACTGGGGTCACGGAATTGTC
upper sequence: GLYMA11G15730.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ12515 (Selaginella moellendorffii), 3'ss of exon 9
agagttgaataatgccagtttaggatggaaccattattttgcaattttgctataaaaactgaaaagactcctagtcctaatgagcccttgtacttggcagTGTTGCAAGATATCAAGAAGCAAATCCTGCAGTTTATACAACTATTATATTCCCATTTCTTTTTGCGGTTATGTTTGGCGACTGGGGTCATGGAATTTGC
| ||| || | || | |||| || | || || || | ||| || |||||||| |||||||||||||||||| || | ||||| || | | | ||| |||||||| || ||||| |||||||| ||||||||||| |||||| |
------------------------------gtaagattgtgaaccattatt-----ggctgacaaaagtctta-------tggtcttttggcctc--cagTGTTGGAAGATATCAAGAAGCAAACCCGGGAGTTTTCACCATCGTGACATTTCCATTTCTATTCGCGGTCATGTTTGGGGACTGGGGTCACGGAATTGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgctataaaaactgaaaagactcctagtcctaatgagcccttgtacttggcagTGTTGCAAGATATCAAGAAGCAAATCCTGCAGTTTATACAACTATTATATTCCCATTTCTTTTTGCGGTTATGTTTGGCGACTGGGGTCATGGAATTTGC
tcctaat putative branch site (score: 2)
cccttgt putative PPT
tataaaaactgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agagttgaataatgccagtttaggatggaaccattattttgcaattttgctataaaaactgaaaagactcctagtcctaatgagcccttgtacttggcagTGTTGCAAGATATCAAGAAGCAAATCCTGCAGTTTATACAACTATTATATTCCCATTTCTTTTTGCGGTTATGTTTGGCGACTGGGGTCATGGAATTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - aatgcca
- - - - - - - - - - - ggatgga
- - - - - - - - - - - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaagac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcccttg