Sequence
atgc intronic sequence ATGC exonic sequence...ctttgataaatctatttctttcattacatatctcttccgctctctcataattaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCACTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
Basic information
species | Glycine max |
transcript | GLYMA17G05550.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05550.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G348602_T01 (Zea mays), 3'ss of exon 1
ctttgataaatctatttctttcattacatatctcttccgctctctcataattaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCACTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
| ||| | | ||| |||| || || || ||||||||| || || |||||| ||||||| |||| || ||||||||||||||| |||||| || || |||| ||| || | |||||||| || ||
-----------------------------------------------------gtgagcttattta-actggcattgtgatgttttctgg------acagGATGAGAAGTACTGGCCATTGATGCCAGCATTACCGTCATATGGGTATGGGCGGGAGCGCAAAGGACCACGATTTGGGAGCCTCATTCATGGACAGAATT
upper sequence: GLYMA17G05550.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G047414_T01 (Zea mays), 3'ss of exon 1
----ctttgataaat--ctatttctttcattacatatctcttccgctctc-tcataattaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCACTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
|||| || || |||| | ||| | | || | | | | | | ||| | | ||| |||| || || || ||||||||| || || |||||| ||||||| |||| || ||||||||||||||| |||||| || || |||| ||| || | |||||||| || ||
cagagtttggtagatgcctatggtgcttatttgggggcacaaatgcccacatttcagattgtgagcttattta-actggcattgtgatgttttctgg------acagGATGAGAAGTACTGGCCATTGATGCCAGCATTACCGTCATATGGGTATGGGCGGGAGCGCAAAGGACCACGATTTGGGAGCCTCATTCATGGACAGAATT
upper sequence: GLYMA17G05550.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G42950.1 (Arabidopsis thaliana), 3'ss of exon 1
----------ctttgat----aaatctatttctttcattacatatctcttccgctctctcat----aattaaacattttactgac------actatatttgtcatcttacgt--gatggctaacagGATGAAAAATATTGGCCACTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
|| |||| || | | | | || |||| || | | | || | || |||| | || | || ||| | | | || | | | |||||||||| |||||| | || | ||||| || ||||||||||| ||||| || ||||||| ||| ||||| ||||| ||||| |||||||| || |||
gttttgtttcctctgatttgaaattgtgatctatgtgtttgggatctgtttagggttttgatgcagagtttgttatttggttcactattgaattaagattgggttttgatgttgaaacgtttttagGATGAAAAGTATTGGTCTTTGCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATC
upper sequence: GLYMA17G05550.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 3'ss of exon 1
---ctttgataaatctatttctttcattacatatctcttccgctctctcataattaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCACTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
|| ||||| |||| | | || || | | | | || |||| || ||| || | | | | || ||||| |||| ||||||||||| || |||||||||||||||||||| ||||||||||||||||||||||| ||||||| ||| |||||||||| |||||||||||||||||| |||
gatattcaataaa-ctatca-tattatgactagtgttagcatttatcgtataagcgaa-gtttggcttattttggttctttcttcttatgtgacatttaacagGATGAGAAGTATTGGCCACTGATGCCTCCCTTGCCTTCATATGGGTATGGGAGAGAGCATCGTGGAGCTCGATATGGGAGTTTGATTCATGGTCAAAATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cataattaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCACTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
ttaaacattttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttgataaatctatttctttcattacatatctcttccgctctctcataattaaacattttactgacactatatttgtcatcttacgtgatggctaacagGATGAAAAATATTGGCCACTGATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - -ctcttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatc