Sequence
atgc intronic sequence ATGC exonic sequencegtgtcgaagatcttgtcataaggggtttcaattactgtatcattgatgaggttgattcaatccttattgatgaagctagAACACCGCTTATTATATCTGGACCTGCAGAGAAACCCAGTGATCAATATTATAAGGCTGCAAAGATTGCAGAAGCCTTTGAACAAGACATACATTACACT
Basic information
species | Glycine max |
transcript | GLYMA02G01060.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 3'ss of exon 3
---------------------------------------------------gtgtcgaagatcttgtcataaggggtttcaattactgt--atcattgatgaggt----tgattcaatccttattgatgaagctagAACACCGCTTATTATATCTG-GACCTGCAGAGAAACCC---------AGTGATCAATATTATAAGGCTGCAAAGATTG--CAGAAGCCTTTGAACAAGACATACATTACACT-----------
|| | | | | | || | | | | |||| || ||| | || |||| | | | ||| |||| | | ||| | | || ||| || | | | | | |||| | | | | ||| | | | | | || | | ||
gtatgctgtttcctttgatagttatttgttaatgcctgattgggcacattcgtctttgaagtgtcataatcacatttccctctccctgtccataggtgaaggagtgcagtgataacagattcacagattctgctaactgattcttcattttttttgcagACTGTTGATGAGCTTGTCCTGAGGAACTTTAACTATTGTGTGATAGATGAAGTTGATTCCATTCTCATTGATGAAGCAAGAACACCTCTTATAATATCAG
upper sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtcgaagatcttgtcataaggggtttcaattactgtatcattg-atgaggttgattcaatccttattgatgaagctagAACACCGCTTATTATATCTGGACCTGCAGAGAAACCC---AGTGATC---AATATTATAAGGCTGCAAAGATTG--CAGAAGCCTTTGAACAAGACATACATTACACT-----------
| || | | | | | | | | | | | |||| ||||| || || || || ||| | ||| || ||| || | || ||| | || ||| | |||| | | || | ||| | | | | | | || | | | ||
--gaaagtaattcttgctttattttctcctttcattat-tgattgtatgagtttattttggatgttttttctga-gttag----tttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
upper sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G01800.2 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------gtgtcgaagatcttgtcataaggggtttcaattactgtat----------cattgatga--ggttgattcaatccttattgatgaagctagAACA-CCGCTTATTATATCTGGACCTGCAGAGAAACCC---AGTGATC---AATATTATAAGGCTGCAAAGATTG--CAGAAGCCTTTGAACAAGACATACATTACACT-----------
|| |||| | || || || || ||| |||| ||| | ||| | || | || | || | || ||| || | || ||| | || ||| | |||| | | || | ||| | | | | | | || | | | ||
gtcaccaacagtgagcttggatttgattatctgagagacaatctagccacggaaagtaattcttgctttattttctcctttcattattgattgtatgagtttattttggatgttttttctgagttagtttctgattgtacagAGTGTTGAGGAGCTCGTCTTGAGGGATTTCAATTATTGTGTGATTGATGAAGTTGATTCCATACTTATTGATGAAGCAAGGACTCCTCTCATTATCTCTG
upper sequence: GLYMA02G01060.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 5
gtgtcgaagatcttgtcataaggggtttcaattactgtatcattgatgaggttgattcaatccttattgatgaagctagAACACCGCTTATTATATCTGGACCTGCAGAGAAACCCAGTGATCAATATTATAAGGCTGCAAAGATTGCAGAAGCCTTTGAACAAGACATACATTACACT
|||||| | |||||||||||||||||| | |||||||||||||| ||||| || ||||| ||||| ||||| || || ||||| || |||||||| || || || |||||| || ||||| |||||||| ||||| |||||||| | ||| | |||||
----------gcttgtcttgaggggtttcaattactgtgtaattgatgaggttgactcaattctgattgacgaagCAAGAACTCCTCTCATTATCTCAGGACCTGCTGAAAAGCCAAGTGATAGGTACTATAAAGCTGCAAAAATTGCCTTGGCCTTTGAGCGAGATCTGCATTA---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttcaattactgtatcattgatgaggttgattcaatccttattgatgaagctagAACACCGCTTATTATATCTGGACCTGCAGAGAAACCCAGTGATCAATATTATAAGGCTGCAAAGATTGCAGAAGCCTTTGAACAAGACATACATTACACT
tattgat putative branch site (score: 3)
ttattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtcgaagatcttgtcataaggggtttcaattactgtatcattgatgaggttgattcaatccttattgatgaagctagAACACCGCTTATTATATCTGGACCTGCAGAGAAACCCAGTGATCAATATTATAAGGCTGCAAAGATTGCAGAAGCCTTTGAACAAGACATACATTACACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC