Sequence
atgc intronic sequence ATGC exonic sequence...ttaattatctactagtacgaggattggtttgttgcaatctgcacgtggataattggtgcaatgtggaatcttacttgatgtgttgaaaatgaaataacagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACTGAGCGTGCTGTGAAGACTTGGCAA
Basic information
species | Glycine max |
transcript | GLYMA10G33590.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G33590.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g43420.1 (Oryza sativa), 3'ss of exon 1
-ttaattatctactagtacga----ggattggtttgt--tgcaatctgcacgtggataattggtgcaatgtggaatcttacttgatgtgttgaaaatgaaataacagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACTGAGCGTGCTGTGAAGACTTGGCAA
| || | | | | | | | || | || | | || | |||| ||| ||| ||| || || || | | | |||||||||||| || |||| | || || ||||| ||||||||||||| |||||||||||| ||| || || || ||||||||||| |||||
tctgatcacacgcgacggcaaattggcaatgctctgcaccgtagcagttacaagactaatcggtagaatacataatttt----gagccctttgcactaacg---cagGAAGCATTGGAAAAGCTGGGTTACTATTCGGGCGAAGAAGACATGGAGTTCTCCAGCTTCTCATCTGGCACCGAACGAGCTGTGAAGACATGGCAG
upper sequence: GLYMA10G33590.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G031721_T02 (Zea mays), 3'ss of exon 1
-------ttaattatctactagtacgaggattggtttgttgcaatctgcacgtggataattggtgcaatgtggaatcttacttgatgtgttgaaaatgaaataacagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACTGAGCGTGCTGTGAAGACTTGGCAA----
| ||| | | || || | ||| | | | | | | ||| || | || || || || | || ||| |||||||| ||| ||| | || |||||||| |||||||||||||||||||| ||||| ||||| ||| || ||||| ||||| ||||| |||||
ccaaggaattcctatttcatcaagagaaaataaactagtttctcttagtaggcaattgtttgt--cagtacaaaaactaacagcattttctgcc--tgacg---cagGAAGCTTTGCAGAAGCTCGGTTTTTACTCAGGCGAGGAAGACATGGAGTACTCCAGTTTCTCGTCTGGCACCGAGCGAGCTGTCAAGACATGGCAGGTTA
upper sequence: GLYMA10G33590.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G031721_T03 (Zea mays), 3'ss of exon 2
-------ttaattatctactagtacgaggattggtttgttgcaatctgcacgtggataattggtgcaatgtggaatcttacttgatgtgttgaaaatgaaataacagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACTGAGCGTGCTGTGAAGACTTGGCAA
| ||| | | || || | ||| | | | | | | ||| || | || || || || | || ||| |||||||| ||| ||| | || |||||||| |||||||||||||||||||| ||||| ||||| ||| || ||||| ||||| ||||| |||||
ccaaggaattcctatttcatcaagagaaaataaactagtttctcttagtaggcaattgtttgt--cagtacaaaaactaacagcattttctgcc--tgacg---cagGAAGCTTTGCAGAAGCTCGGTTTTTACTCAGGCGAGGAAGACATGGAGTACTCCAGTTTCTCGTCTGGCACCGAGCGAGCTGTCAAGACATGGCAG
upper sequence: GLYMA10G33590.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0051g00860.t01 (Vitis vinifera), 3'ss of exon 1
ttaattatctactagtacgaggattggtttgttgcaatctgcacgtggataattggtgcaatgtggaatcttacttgatgtgttgaaaatgaaataa------cagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACTGAGCGTGCTGTGAAGACTTGGCAA
| ||| | | | ||| || ||| || | | | | ||| | || | | | ||| || || | | | ||||||||| | || ||||| ||||| ||||| |||||||| |||| | |||||||||||||||||| |||||| | ||||| || ||||||||
-----tgtctttctttttgttttgtttttttttctaatatgatctaacactttcctggtgatg-atattccaattgggtgtatttgaactagtgtgattttgacagGAAGCACTTCAAAATTTGGGATTTTATTCTGGTGAGGAAGATGTGGAATTTTCCAGCTTCTCAAGTGGGACTGAGAGAGCTGTAAAAACTTGGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggataattggtgcaatgtggaatcttacttgatgtgttgaaaatgaaataacagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACTGAGCGTGCTGTGAAGACTTGGCAA
ttgaaaatgaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaattatctactagtacgaggattggtttgttgcaatctgcacgtggataattggtgcaatgtggaatcttacttgatgtgttgaaaatgaaataacagGAAGCATTGTTGAAATTGGGGTTTTACTCTGGCGAGGAAGACATGGAGTATTCCAGCTTCTCAAGTGGAACTGAGCGTGCTGTGAAGACTTGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - tgcaatc
- - - - - - - - - - - - - - - - - - - -tgcacgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa