Sequence
atgc intronic sequence ATGC exonic sequence...gtatgtgtttgctctttaaaccaatatttaattaccatggtttaatgaaaactggactattggcatattatattcatacatgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG
Basic information
species | Glycine max |
transcript | GLYMA03G34140.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G34140.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g15490.3 (Oryza sativa), 3'ss of exon 4
-----------------gtatgtgtttgctctttaaaccaatatttaattaccatggtttaatgaaaac-----tggactattggcatatt-atattcatacatgtgtgct---cctacc------------------ttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG
| | | |||||||| ||| | || | || ||| | ||| | | ||| || | |||| || | | || | | | |||| ||| ||||||||||||| || ||||| |||||||||||||| ||||| |||||||||||| | ||||| || || || |||||||||||
gtaattttcttgttcccttgtttagttgctcttcaaatctcgatagacttgttatg-tccaatcctcatgcccatagacctttcacttattgatgtccctagactcccgataaacctattacttactacagtttgggattatagGTTGGTCAAGAGCAGTTCTCGCCTAGTTCACCTGGCTGGCCTCCTTTCATGAGGGTCAATCCTATATTGGACTGGTCATACAG
upper sequence: GLYMA03G34140.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G381933_T03 (Zea mays), 3'ss of exon 4
----------------------------------gtatgtgtttgctctt--taaac-caatatttaattaccatggtttaatgaaaactggactattggcatattatattcatacatgtgtgctcctacctt-------acagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG
| |||| | | | || |||| ||| | ||||||| | | | || || ||| | | | || || | | || | |||||||||||||||| ||||| |||||||||||||| ||||| ||||| |||||| ||||||| || || ||||||||||||||
gtgattttcttttaccattgctcatttgttgttaacaaccccttgcacctattgtacgcaatgatta-tgcccatggtgttcccagttccttacagttttggtatctcactgaactttgagtaaacacaattttgaaatgatagGTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATGAGGGTGAATCCAATCTTGGATTGGTCATACAG
upper sequence: GLYMA03G34140.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G028010_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------gtatgtgtttgctctttaaaccaatat-ttaatt---accatggtttaa-----tgaaaactggactattggcatattatattcatacatgtgtgctccta---ccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG
|| | | | | | | ||| | || |||| | || || | || | || ||| | || | || ||||| | ||| ||||||||||| || | ||||||||||| || |||| ||||| |||||||||||| |||| || || || |||||||| |||||
gtgactccccttgaattgagtgctcccgttttagtctacttcactgtcgtcattctacacctctatcgatctagctagtatactggttcatgccattctgcaacattttgggggccgggttcatgacatgtgatggtaattgcggtgtggaaaaaaatacttgtagGTTGGTCAACAAGAGTTCTCCCCTAGCTCGCCTGACTGGCCTCCTTTCATGAGGGTGAACCCTATCTTGGATTGGTCCTACAG
upper sequence: GLYMA03G34140.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G149609_T01 (Zea mays), 3'ss of exon 4
gtatgtgtttgctctttaaaccaat---atttaattaccatggtttaatgaaaact----------ggactattggca-tattatattcatacatgtgtgctcctacc-ttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG
||| | | ||| || | ||| | | ||| | ||||| || | || |||| || | || || |||| | | |||| |||||| || | ||||||||||| || || || ||||| |||||||||||| |||| || || || |||||||| |||||
----gtgacttcccttgaatcgaatgacgcctgcctgacataatcgaatgacaatttttttttgagggttcattgatggtaatctaatcgcg-gtgtgaatgaaaattgctgtagGTCGGTCAACAAGAGTTCTCCCCTAGCTCGCCCGGCTGGCCTCCTTTCATGAGGGTGAACCCAATCTTGGATTGGTCCTACAG
upper sequence: GLYMA03G34140.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgtgtttgctctttaaaccaatatttaattaccatggtttaatgaaaactggactattggcatattat-attcatacatgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG
||| ||| | | ||| || | | || | | | || | | | || || ||| || | | | | || |||||||||||||| |||||||| |||||||||||||| ||||| || || |||||| ||||||| || || |||||||| |||||
------gttagct--tcacttcaaatctttaatctcaagatccagatgcaaatattttgtgatagtaaaatgattgattacttcttaatgcattttttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG
upper sequence: GLYMA03G34140.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------gtatgtgtttgctc----tttaaaccaatatttaattaccat---ggtttaatgaaaactggacta------ttggcatatta--tattcatacatgtgtgctccta------ccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG
||| ||| |||| ||| | ||| | |||| | | | ||| || | || | || | | || | || || || | | | || ||| ||||| ||||||||||||||||| |||||||||||||| ||||||||||| ||||| |||| || || || |||||||| |||||
gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcctcatactagattatcttccagatttctgtaagattgcattagaagattcaaagtgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaactggactattggcatattatattcatacatgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG
ctcctacctt CT-rich tract
atattatattcataca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgtttgctctttaaaccaatatttaattaccatggtttaatgaaaactggactattggcatattatattcatacatgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG
- - -tgtttgc
- - - - - - - - - - - - - - - - - ccatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgct