Sequence
atgc intronic sequence ATGC exonic sequence...atgtgctacaccttttcctatatttgtcttttggagttaatgtttcagttgtcgagctgtctccttttgatgcatgatttttgaactttacaacttgcagGTATTGGAGGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAACTTATGTTATT
Basic information
species | Glycine max |
transcript | GLYMA04G38800.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38800.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 3'ss of exon 14
atgtgctacaccttttcctatatttgtc-ttttggagttaatgtttcagttgtcgagctgtc-tccttttgatgcatgatttttgaactttacaacttgc--agGTATTGGAGGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAACTTATGTTATT
|| | | | || | | | | || | | | | ||| |||||| || | | | | | || |||| || | | || |||| |||||||||||||||||||||||||| ||||| ||||| ||||| || ||||| || ||||||||||| || |||||||| |||||| |||| || |
---tgtttctaatggtcgtgcaatgagcattctagctacattccttctgttgtccagttattatttatcttatat-caatttatgccttccttcatttttttagGTTTTGGAGGCAAGGGCTGGATTTTATGAGAAACCCATTGCGACTTTGGACTTTGCTTCGTTGTATCCATCCATCATGATGGCATATAACCTATGCTACT
upper sequence: GLYMA04G38800.1 (Glycine max), 3'ss of exon 14
lower sequence: AT5G63960.1 (Arabidopsis thaliana), 3'ss of exon 14
----atgtgctacaccttttcctatatttgtcttttggagttaatgtttcagttgtcgagctgtctccttttgatgcatgatttttgaacttta--caacttgcagGTATTGGAGGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAACTTATGTTATT
|| | | | ||| || ||||||| | ||| || | | |||| | || | || ||| | | | | | | ||||| || || ||||| | || || |||||||| |||||||| ||||| |||||||| || |||| || || ||||||||||| ||||| | || || |
gtaagtgggtgatttatggatctaacatttccttttggcctatcggttgcattaattccactgttccgacatgtttgttgttttggatatgtcaaacgatattcagGTTTTAGAAGCAAGAACAGGTTTCTATGAAAAGCCAATTGCAACTTTGGATTTTGCTTCACTGTACCCGTCAATTATGATGGCATATAATCTGTGCTACT
upper sequence: GLYMA04G38800.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ15982 (Selaginella moellendorffii), 3'ss of exon 13
atgtgctacaccttttcctatatttgtcttttggagttaatgtttcagttgtcgagctgtctccttttgatgcatgatttttgaactttacaac-ttgcagGTATTGGAGGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAACTTATGTTATT
| ||| || | ||||||| | ||| | ||| | | | || ||||| | || ||||||||||||||||| ||||| |||||||| || | ||||||||||| |||| ||||| ||||||||||| || || | || ||||
-------------------------------------------gtaagtagttcgg------gcttttgaatcgatttttataaacgctgctgcgttacagGTTCTAGAAGCAAGGGCTGGATTTTACGAAAAGCCAATTGCCACGCTTGATTTTGCATCACTGTACCCATCAATTATGATGGCTTACAATCTTTGCTATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttgtcgagctgtctccttttgatgcatgatttttgaactttacaacttgcagGTATTGGAGGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAACTTATGTTATT
ttttgat putative branch site (score: 4)
atttttgaacttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtgctacaccttttcctatatttgtcttttggagttaatgtttcagttgtcgagctgtctccttttgatgcatgatttttgaactttacaacttgcagGTATTGGAGGCAAGGGCTGGATTTTATGAAAAACCAATTGCTACTTTAGATTTTGCATCCTTGTATCCATCTATTATGATGGCCTATAACTTATGTTATT
- - -ctacacc
- - - - - - - - - - - - - -cttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgat