Sequence
atgc intronic sequence ATGC exonic sequence...atttcctttagtttttttttcatatgaatatgaattcacattattgatctgtcttcaaggtcacttattcgtattttgttcttatctatgagttaaacagGTTCAAGAAAAGAAGGTCAAGAAAGTTTCTGACATGAATGTTGATCCTAAAGCAATGGGAAATGGCTCTATTGCTAGTTCAAGTAATTCCAGTAGCTCCA
Basic information
species | Glycine max |
transcript | GLYMA07G01440.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g41630.1 (Oryza sativa), 3'ss of exon 4
----------atttcctttagtttttttttcatatgaatatgaattcacattattgatctgtcttcaaggtcacttattcgtattttgttcttatctatgagttaaacagGTTCAAGAAAAGAAGGTCAAGAAAGTTTCTGACATGAATGTTGATCCT---AAAGCAATGGGAAATGGCTCTATTGCTAGTTCAAGTAATTCCAGTAGCTCCA
| || ||||| | ||| || | | ||| ||| || | | | | | || | |||| || |||| | | |||||||||||||||||||||| || || ||||| |||||| | ||| || ||| | |||||| |||| | |||||| | ||| | || |
aggtttatttgctaccaaaagtttgccctggcaatggat-tattcttttattcttgtacttacctgagctatattaatcggagttttttttttatttgt---------agGTTCAAGAAAAGAAGGTCAAAAAGGTATCTGAGATGAATTTGAGCCCTTCAAATGCATCTGCAAATGGTAGACCTGCTGGC---AGTAATGCTAGTGGTTCGA
upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------atttcctt-tagtttttttttcatatgaata---------tgaattcac--attattgatctgtcttcaaggtcacttattcgtattttgttcttatctat----gagttaaacagGTTCAAGAAAAGAAGGTCAAGAAAGTTTCTGACATGAATGTTGATCCT---AAAGCAATGGGAAATGGCTCTATTGCTAGTTCAAGTAATTCCAGTAGCTCCA
|||| | || || | | | || | | || ||| | || |||| | | | | || | ||| | | ||| | || | |||||||| |||||||||||||||||||| |||||||||||||| | |||||| |||||| | ||||||||| | |||||||||||||||| || | ||
gtaggaagggaaaattgtcttatgaaactttaaacttcctgatttttaatttgttgacagattatgctcaacatcaccaactccagtttggtttctttaactactgatataatatatatcctgcacatgctgattacatagctgtcttttcgagaatgaaacagGTCCAAGAAAAGAAGGTCAAGAAGATTTCTGACATGAATTTGGATCCTTCAAAAGCAGTAGGAAATGGCAGTGTTGCTAGTTCAAGTAACTCAACAAGTC---Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|22525826|gb|BU084637.1|BU084637EST: AAACCATCAAATTTTGGAAG GTTCAAGAAAAGAAGGTCAAGAAAGTTTCTGACATGAATGTTGATCCTAAA
genomic: AAACCATCAAATTTTGGAAGgtatgaaatg ... agttaaacagGTTCAAGAAAAGAAGGTCAAGAAAGTTTCTGACATGAATGTTGATCCTAAA
EST:
gi|33389971|gb|CA853178.1|CA853178EST: GTGCTTTGTTCCTTCTATCCACAAATGATAAAACCATCAAATTTTGGAAG GTTCAAGAAAAGAAGGTCAAGAAAGTTTCTGACATGAATGTTGATCCTAAA
genomic: GTGCTTTGTTCCTTCTATCCACAAATGATAAAACCATCAAATTTTGGAAGgtatgaaatg ... agttaaacagGTTCAAGAAAAGAAGGTCAAGAAAGTTTCTGACATGAATGTTGATCCTAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatctgtcttcaaggtcacttattcgtattttgttcttatctatgagttaaacagGTTCAAGAAAAGAAGGTCAAGAAAGTTTCTGACATGAATGTTGATCCTAAAGCAATGGGAAATGGCTCTATTGCTAGTTCAAGTAATTCCAGTAGCTCCA
tattgat putative branch site (score: 3)
tattttgttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttcctttagtttttttttcatatgaatatgaattcacattattgatctgtcttcaaggtcacttattcgtattttgttcttatctatgagttaaacagGTTCAAGAAAAGAAGGTCAAGAAAGTTTCTGACATGAATGTTGATCCTAAAGCAATGGGAAATGGCTCTATTGCTAGTTCAAGTAATTCCAGTAGCTCCA
- - - - - - - - - - - - - - - - -attcaca
- - - - - - - - - - - - - - - - - - - - - - - - ctgtctt