Sequence
atgc intronic sequence ATGC exonic sequence...actgagctggtgaaacagattaaaatatgtgtatttcatctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
Basic information
species | Glycine max |
transcript | GLYMA05G30210.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g07670.1 (Oryza sativa), 3'ss of exon 1
actgagctggtgaaacagattaa--aatatgtgtatttca--tctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgt-tgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
| | ||| | ||| | | ||||| || | || | ||| | | |||| | | | ||| | | | | | | | || | ||||||| || ||| |||| |||||| || |||||||||||||| || ||||| || |||||||||||||| ||||||||| ||||||| ||||||||||| |
----ctttcctaaaataaattcattattatgtttaccataattccatggtagaactttgtgagct-caacagttctcatctgccttttatgcttcttatatgcagTACAAAGTTGAAGAACCAGTTAAGCTCTGGGTGAACAAAGTCGGCCCTTACAATAATCCACAAGAAACTTACAACTATCACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 1
actgagctggtgaaacagattaaaatatgtgtatttcatctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
| || | | || |||| | ||| | || | | || | ||| |||| ||| ||||||| || ||| ||| ||||| || ||||| ||||| ||||| || || || || || |||||||| ||||||||||||||||||||||||||||| |
gccatttctaaaaactaagcctactgatttgtaatcacactgagaacaacttttgtatgttagtaatcacttcatctacctgttatttaattttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTACAATAACCCGCAAGAAACTTACAACTATTACAGCCTCCCATTTTGTCAGC
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 1
actgagctggtgaaacagattaaaata-tgtgtatttcatctgtagtatcaagtggtgaacagcttctgtttttaaacgg------atgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
| | | | || || ||||||||| | || || | || |||| | | ||| ||| || ||||| | |||| ||| || || | |||| || ||||||||||| ||||| || || ||||| ||||| ||||| |||||||| |||||||| || ||||| ||||
------tttaggtgatattttggcctactgtgtattttggaggaagaatgtgtttgtctggtgctttggaacatttacgatgtgtcgtgttcttcgctttgt-gtagTACCAATCGGAGGAGAAGGTTATGCTCTGGGTGAACAAGGTTGGCCCGTACAACAACCCACAGGAAACTTACAACTACTACAGCCTTCCGTTTTGCCATC
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G420310_T01 (Zea mays), 3'ss of exon 1
-actgagctggtgaaacagattaaaatatgtgtatttcatctgtagtatcaa-gtggtgaacagcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
| || ||| | || | | || | | || || || || | | ||| | | | | | | | || ||||||| || ||| || | |||||| ||||||||||| |||||||| ||||| |||||||| |||||||| |||||||| |||||||| ||||||||||| |
gattg--ctgcttgaatgttgttttccttatgcttcctacatgctgtgcaaatatgttccgtactcaaaatttctcatccctttcaatgcttcttaatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAACAATCCTCAAGAAACTTACAACTACTACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G026231_T01 (Zea mays), 3'ss of exon 1
--actgagctggtgaaacagattaaaatatgtgtatttcat-ctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
|||| ||| | | || |||| | | ||| | || | | | ||||| ||| | | | | || | || ||||||| || ||| || | |||||| ||||||||||| |||||||| ||||| || ||||| |||||||| ||||||||||||||||| ||||||||||| |
ttgctgattgagtg---ctgttttctttatgcttcctacatgccgtgcaaatattttctgaactcaaaaagttctcattccttttaatccttcttacatgcagTACAAAACTGAAGAGCCAGTTAAGCTTTGGGTGAATAAAGTTGGCCCTTACAATAATCCTCAAGAAACCTACAACTATTACAGCCTTCCATTTTGTCAAC
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 1
actgagctggtgaaacagattaaaatatgtgtatt--tcatctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
| ||| | | | |||| | | | | | |||| ||| || | ||| | | || ||| ||| || |||| ||| | || | || | || ||||||||||| |||||||| || |||||||| || || ||||||||||| ||||||||||||||||| |||
gcccagc-gctagataggatttttacgtttttgccaacaagctgtctaatcgttctcatccatgcgctttctttctttctgctgctgtttgttt-attttagTACCAAGCAGCGGAGCCTGTGACGCTCTGGGTGAACAAGGTTGGTCCGTACAACAATCCGCAGGAGACATACAACTACTACAGCCTCCCATTTTGCCATG
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G087212_T01 (Zea mays), 3'ss of exon 1
actgagctggtgaaacaga-ttaaaatatgtgtatttcatctgtagt-atcaagtggtgaacagcttctgtttttaaacggatg-tattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
|||| |||| || | | | || | || | || | | | | | || || | | || |||||| || |||||||| || || |||| ||||| || ||||| ||||| ||||| ||||| || || || |||||||| |||||||||||||| ||||| |||||||| |
---ttgctgtcttttcagaatttacctgcactgaatttaactatgacgataatgcctttacctactaaatcattgcagcttataatatttttcttatgtgcagTATAAAACAGAAGAACCTGTTAAGCTATGGGTAAACAAGGTTGGGCCTTACAATAACCCTCAAGAAACTTACAACTATTACAGTCTCCCGTTTTGTCAAC
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 1
actgagctggtgaaacagattaaaatatgtgtatttcatctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttg-----ttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
|| | || | | | | || | || | | |||| | | | || || | |||| || || ||||||||| || || || || | ||| ||||| ||||||||||| || ||||||||||||||||||||||||||||||||||| || |||||||| | |
---gaattt-tggttcttactctctcttactagttaatcccataaacttttacatttctgtgctttt-ctgtcaagtcaattttttttgccttcacctttttcagTATCAAGCCGAGGAGCAGGTCACCCTATGGGTAAACAAAGTTGGCCCATATAACAATCCACAAGAAACATACAACTATTACAGTCTTCCATTTTGCCGCC
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 1
actgagctggtgaaacagattaaaatatgtgtatttcatctgt---agtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgt--tgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
|| || | | ||| | ||| | || | | | | ||| | | | | || | || | | ||||| ||| | |||||||||| ||||| || || | || ||||| ||||||||||||||||| || |||||||||||||| |||||||| | |||||| ||||||||||| |
----agacactggctctg-ttacagtattcatgaaacacttaactgggaaatatgtgacttaaacataatattgtataaggaaatcatttttgtttctcctgcagTATCAGACAGATGAGCAGGTGACTCTGTGGGTAAACAAAGTTGGTCCTTACAATAATCCACAAGAAACCTACAACTACTTCAGCCTTCCATTTTGTCACC
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 1
actgagctggtgaaacagattaaaatatgtgtatttcatctgtagtatcaagtggtgaac-agcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
| || || | || || || | | | || | || | || | | ||| | ||| | | | | | || | ||||||||||| || |||||| |||| ||||||||| || || ||||| ||||| || |||||||||||||| ||||| ||||| || || |||||||||| ||
atgctacttctgtacttactttctgtaagta-gctcaaattacagctcttgcttttgttccagatgcactttgttaacagttttttaattttgtcttgcagTATCAGCAGAATGAACCGGTTACCCTTTGGGTAAATAAGGTTGGACCTTACAATAATCCACAAGAAACGTACAATTATTATAGTCTTCCATTTTGTCGTC
upper sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S438_26V6.1 (Physcomitrella patens), 3'ss of exon 1
--actgagctggtgaaacagattaaaatatgtgtatttcatctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
| || || | || | | | || || | | ||| | | | | | | || || | | | || | || | |||||||| | | || | || | || |||||||||||||| || ||||| |||||||| ||||| || |||||||| ||||| || || ||||| ||
ggaacga-tcggggtgccatgtcagcacctgcacatggc-tttgtgatgacgaactgggccgcggttgtgatgggtgaggtccgtgtgttgtgagtgtgcagTATGGCAAAGGGGATCCGGTGATGCTGTGGGTGAACAAAGTGGGGCCTTACAACAATCCGCAAGAGACGTACAACTACTACAGTCTGCCGTTTTGCAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
ttttatttt CT-rich tract
atgtattttattttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgagctggtgaaacagattaaaatatgtgtatttcatctgtagtatcaagtggtgaacagcttctgtttttaaacggatgtattttattttgttgcagTATCAACATGATGAACAAGTTAACCTTTGGGTGAACAAAGTTGGTCCTTATAACAATCCACAAGAAACATACAACTATTACAGCCTCCCATTTTGTCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - -gctggtg
- - - - - - - - - - - - -tatgtgt
- - - - - - - - - - - - - - - - - - catctgt
- - - - - - - - - - - - - - - - - - - - - - - - - agtggtg