Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatttattttctgtctgtgttcattttatttttctgtctatgatatcaatttgcttcattttgatggaatagAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTCCGCAACATGATTATTGTGCCTGAGATGATTGGTAGCATCATTGGAGTCT
Basic information
species | Glycine max |
transcript | GLYMA07G39980.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G39980.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g04790.t01 (Vitis vinifera), 3'ss of exon 3
------------------gtatgtatttattttctgtctgtgttcatttta-----tttttctgtctatgatatcaatttgcttcattttgatggaatagAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTCCGCAACATGATTATTGTGCCTGAGATGATTGGTAGCATCATTGGAGTCT
|| || | | || | | || || || | | ||| |||| | | | || | ||||| | || || ||| | |||||||||||||||||||| | |||||||| ||||| ||||| || || ||||| |||||||| ||||| ||||| || |
aattttctgtagtattttgttaatagtcaattatgagttacgagggttatagaaacttgcttcagccttgactgatttttgtggtaatgttttgaatcagAAACGTGAGGCCCCACCTGGTGAGAAGCCAGAACCAGTCAGAACCCATCTGCGCAATATGATCATCGTACCTGAAATGATTGGAAGCATTATTGGCGTGT
upper sequence: GLYMA07G39980.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S47_42V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------gtatgtatttattttctgtctgtgttcattttat---ttttctgtctatgatatcaatttgcttcattttgatggaat---agAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTCCGCAACATGATTATTGTGCCTGAGATGATTGGTAGCATCATTGGAGTCT
||||| | || | || | || | | | || || | || | | | | ||| ||||| | || ||||| || ||||||||||| || || || | || || |||||||||||||| ||||| || |||||||| |||||| ||||||| || |
gtacgttaaatacttccactctgatcctggttgttttataaactccttttgccatgagccatggagtattgaaagtcatgcggtataacacttgtgagtctcatggacatacagtatcttgataccctctctgtataattgcagAAACGTGAGGCACCTGCTGGTGAGAAGCCTGAGCCTGTGAGGACACACCTCCGCAACATGATCATTGTTCCAGAGATGATCGGTAGCGTCATTGGTGTGT
upper sequence: GLYMA07G39980.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S223_96V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------gtatgtatttatttt-ctgtctgtgttcattttatttttctgtctatgata--tcaatttgcttcattttgatgga---------------atagAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTCCGCAACATGATTATTGTGCCTGAGATGATTGGTAGCATCATTGGAGTCT
||| ||||| | | || | | || || | || | | | | |||| ||| || ||||| | |||| | || ||||| | ||||| ||||| || || || | || || ||||| |||||||| ||||| || ||||||||||||||| ||||||| || |
gtatgatagtctttccgcttttttgtatctcgttctaaaagagttgtgtgaattacatcgacttcaaattgttgacattttaccgactttttcaatcttgtgcgcctattttcgtcaggtcaacatgcagtgttctgatgaccttactctactttttacagAAGCGTGAGGCACCTACCGGTGAAAAGCCCGAGCCTGTGAGGACTCACCTCCGTAACATGATCATTGTCCCGGAGATGATTGGTAGCGTCATTGGTGTGT
upper sequence: GLYMA07G39980.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26930 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtatttattttctgtctgt-gttcattttatttttctgtctatgatatcaatttgcttcattttgatggaatagAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTCCGCAACATGATTATTGTGCCTGAGATGATTGGTAGCATCATTGGAGTCT
| || | | || ||| || || || | | ||| ||| | | | | |||||| | || || || || ||||||||||| || ||||| || || |||||||| | |||||| || || || ||||||||||| ||||||||||| ||||
-------------gtaagttcatcgatcttttctttgttttgcttttcttattgattccttgtgtcct----gcgtagAAACGTGAGGCCCCGGCTGGTGAGAAGCCCGAGCCAGTGCGAACGCATCTCCGGAGCATGATCATCGTCCCAGAGATGATTGGCAGCATCATTGGCGTCT
upper sequence: GLYMA07G39980.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26636 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtatttattttctgtctgtgttcattttatttttctgtctatgatatcaatttgcttcattttgatggaatagAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTCCGCAACATGATTATTGTGCCTGAGATGATTGGTAGCATCATTGGAGTCT
|| ||| || | || ||| ||| ||| | | || ||| | | || | |||||| | || || || || ||||||||||| || ||||| || || |||||||| | |||||| || || || ||||||||||| ||||||||||| ||||
--------gtaagttc-atcgatcttttctttgtttctcttttctt---attgattccttgtgtctt----gcgtagAAACGTGAGGCCCCGGCTGGTGAGAAGCCCGAGCCAGTGCGAACGCATCTCCGGAGCATGATCATCGTCCCAGAGATGATTGGCAGCATCATTGGCGTCTMapped 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|15662233|gb|BI699604.1|BI699604EST: GAGGTCTCACCAGAAAGCCCATGGCCTTGATTAAAAAGCTCCGCAAAGCG AAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTC
genomic: GAGGTCTCACCAGAAAGCCCATGGCCTTGATTAAAAAGCTCCGCAAAGCGgtatgtattt ... gatggaatagAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTC
EST:
gi|17152865|gb|BM142798.1|BM142798EST: GAGGTCTCACCAGAAAGCCCATGGCCTTGATTAAAAAGCTCCGCAAAGCG AAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTC
genomic: GAGGTCTCACCAGAAAGCCCATGGCCTTGATTAAAAAGCTCCGCAAAGCGgtatgtattt ... gatggaatagAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcattttatttttctgtctatgatatcaatttgcttcattttgatggaatagAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTCCGCAACATGATTATTGTGCCTGAGATGATTGGTAGCATCATTGGAGTCT
ttttgat putative branch site (score: 4)
attttatttttctgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatttattttctgtctgtgttcattttatttttctgtctatgatatcaatttgcttcattttgatggaatagAAAAGGGAAGCACCAGCAGGTGAGAAGCCAGAACCAGTTCGCACCCATCTCCGCAACATGATTATTGTGCCTGAGATGATTGGTAGCATCATTGGAGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG