Sequence
atgc intronic sequence ATGC exonic sequencegtaagggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCCGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
Basic information
species | Glycine max |
transcript | GLYMA07G11880.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
----------------------------------gtaagggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCCGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
|| | | || | | | || | ||| || | | |||| || ||||| ||||| |||||||| | || || || || || ||||||||||| || || ||||| |||||||| ||||| |||||||| ||||| | ||
gtgcgaaatgttgcttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacatttttccgtgtgttattaa-agCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 3
----------------gtaagggtgccttttct-gactatgtt------acctttgtcttgccgtccattcgtttacgatattttc--------agATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCCGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
|| | | |||| || || || || | || | |||| || || | || ||||| ||||| |||||||| || || || ||||| || ||||||||||| || || ||||| ||||| || || || |||||||||||||| | |||
gtgagaacttgtttccccaatgcttttccttctcaaccatcttttgggaactccagctaaaaattctgaacacttacaattttgttgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT
upper sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------------gtaagggtgccttttctgac-tatgttacctttgtcttgccgtccattcgtttacgatattttc--agATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCCGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
|| | | | | || || || | || | || || | ||||||| || ||| |||||||| |||||||| |||||||| |||||||||||||||||||| || || ||||||||||| || ||||||||||||||||||| |||||
gtataagtgtctttctaattcgttgatgtcgctaatttctgatttctatctatctatctatctatctatatatatatatatatgcacacacatttttttctagttacaagttttggtctttctctgtattttctcagCTCCAGGAGATGGCCCAATTGTATTAGTTTTAGCTCCAACTCGTGAACTTGCTGTTCAGATACAACAAGAAGCAGCTAAATTTGGTGCATCATCGAGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCCGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
ttctgac putative branch site (score: 2)
tattttc putative PPT
atattttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCCGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG