Sequence
atgc intronic sequence ATGC exonic sequencegtcaaggcttctcttcccctattttaacatctgaaatcaatagatggtttctttgcaatattattagtaatgttaatagttttctttcattaatacagTTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAG
Basic information
species | Glycine max |
transcript | GLYMA05G27240.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 8
gtcaaggcttctcttcccctattttaacatctgaaatcaatagatggtttctttgcaatattattagtaat-gttaatagttttctttcattaa--tacagTTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAG
|| || | || | | || | | | | |||| | | | || | | || ||| || | ||||| | |||||||||||||| |||||||| |||||||| || ||||| ||||| |||
gttaaaaactgatttatattctgggtgtttccctttcccacaatttgttttctatatctgtagttctcacccactgatcccaaccttggttttacctacagCTTAAGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 8
gtcaaggcttctcttcccctattttaacatctgaaatcaatagatggtttctttgcaatattattagtaat-gttaatagttttctttcattaatacagTTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAG
|| |||| | | || | | || ||| ||| ||| | | || | || | || | ||| |||| | |||||||||||||||| || || || ||||| || |||||||| |||||||||||||||
gtgaaggatagattgtttgtagct-attccttgtaat----------tttttttata-tgttgtctgtccttactagcaagttttcctcataattacagTTGAAGACTGAATGCGGAAGTCAGTTTACTAACAAACTTGAAGGAATGTTTAAG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S70_181V6.1 (Physcomitrella patens), 3'ss of exon 8
gtcaaggcttctcttcccctattttaacatctgaaatcaatagatggtttctttgcaatattattagtaatgttaat--agttttctttcattaatacagTTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAG
| | || ||| || | | || || | | | || || || | | | || | || | | | || | || ||| | ||||| || ||||| || ||||||||||||||||||||||||||||| |||
actcattaatttcatcctacatgatgttagcttaagaccactggtgaattattcggtctcatggatgtgtttctatttgaatgttgtactcttttgtcagCTCAAGACGGAATGTGGGAGTCAGTTCACAAACAAACTGGAAGGAATGTTCAAGMapped 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|31561323|gb|CD487161.1|CD487161EST: TTTTAGGAAAGAGTGCTTCTATTGACGCTGAGAAATCTATGATCTCCAAG TTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTT
genomic: TTTTAGGAAAGAGTGCTTCTATTGACGCTGAGAAATCTATGATCTCCAAGgtcaaggctt ... attaatacagTTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggtttctttgcaatattattagtaatgttaatagttttctttcattaatacagTTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAG
cattaat putative branch site (score: 3)
ttttctttcatt CT-rich tract
aatattattagtaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaaggcttctcttcccctattttaacatctgaaatcaatagatggtttctttgcaatattattagtaatgttaatagttttctttcattaatacagTTGAAGACTGAGTGTGGCAGCCAGTTCACAAACAAACTGGAAGGAATGTTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA