Sequence
atgc intronic sequence ATGC exonic sequence...taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaaacattcaccatattacaaatactgattcccttttttgtgctttccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
Basic information
species | Glycine max |
transcript | GLYMA18G47660.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 3
taattttggt-cttgatatagtttatatatcatatatgtacttgtgcatttaaacattcaccatattacaaat-actgattcc-cttttttgtgctttccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
|||| | | | ||| | || ||| || |||| | ||| | | | || || | || || | | ||| ||| | ||| ||||| ||||||||||| ||||| |||||||||||||| ||||||| |||||| || || |||| || |||| ||||| |||| ||||| ||
taatgtagctgcttaaagctgtctat-tagtatatcttatctttgacgacttagcag-cattgttttctgtattatttattgtgcttcaccttttttttcagTATTATTTGAAGACTGGAACATGCAAATTTGGAGCAACATGCAAGTTTCACCACCCCCGAGAAAAAGCTGCAATTGCAACCCGAGTACAGCTGAATGCTT-
upper sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G146514_T02 (Zea mays), 3'ss of exon 3
taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaa--acattcaccat-attacaaatactgattcccttttttgtgctttccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
|||||| ||| || |||| || | | | | ||| ||||| | | | || | ||| || | | || |||||||| ||||||| || || ||||| |||||||| || |||| |||||||||||| |||| ||||||| || || ||||| ||||||
--attttgtccttttctatgtgagcatataatttcttttggaaagtgtttggttacattattggtgaatttgcatttttattgttttcatacccccttttagTACTATCTGAAGACTGGCACGTGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGTTGAATGAAC-
upper sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G100794_T01 (Zea mays), 3'ss of exon 3
-taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaaacattcaccatattacaaatactgattcccttttttgtgctttccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
| || || | || | | | ||| | || || || | | | | | | | || | | | |||| |||||||| ||||||| || || ||||| |||||||| || |||| |||||||||||| |||| ||||||| || || ||||| |||||
ttgcttgcacattttctgcttttcttttctgtgttattatatcgttttttggaaagtgtatggtcacattatttattgttttcacatccctcctttttagTACTATCTGAAGACTGGCACATGCAAGTTTGGAGCAACTTGCAAGTTTCATCATCCCCGAGAAAAGGCTGCAATGGCAACTCGAGTTCAGCTGAATGAAC-
upper sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02830.1 (Arabidopsis thaliana), 3'ss of exon 3
----taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaaacattcaccatattacaaatactgattcccttttttgtgctttc----------------cagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
||| || | ||| | || || | ||| || | | | ||| | | ||||| | ||| | | ||||||| | | ||||||||||||||||||||||| ||||| ||||||| ||||| | |||||||||||| || |||| |||||||||||||||||||| | | ||||| |
gtaagaatctttggtttgtccagttgtagatgaacattttgtcaaggtttggtaattgagtcatcttcttacacaaactaacttaacattttgtggtgttgtatgttttggttgcgcagTACTATTTGAAGACAGGAACCTGCAAGTTTGGAGTAACATGTAAGTTTCATCATCCAAGGAACAAAGCTGGGATTGCTGGAAGAGTCTCTCTCAATATGT-
upper sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G16540.2 (Arabidopsis thaliana), 3'ss of exon 3
taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaaacattcaccatattacaaatactg-attcccttttttgtgctt-tccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
| | || | ||| ||||||| ||| || || | |||| | | |||| | ||| || ||||| | | |||| ||| |||||||||| || |||||||| |||| || |||| ||||||||||||||| |||| ||||| |||| |||||| || | | ||| | |
-----gtagctctgtttcgaattac-tatcata---gta---atgtcttctagttatcacattgtctcaaagcttctatttttgttgttgtgtctgtgcagTTTTATCTGAAGACAGGGACCTGCAAATTCGGAGTGACTTGCAAGTTTCATCATCCTAGGAACAAAGCTGGTATTGATGGAAGTGTATCAGTTAATGTCT-
upper sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 3
taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaa-acattcaccatattacaaat--actgattcccttttttgtgctttccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
|| ||| | |||| | | || | ||| | || | ||||| | ||| | | | | || ||| |||| | | |||||||||| |||||||||||||||||||| |||||||||||||||| ||||||||||||||||||||||||||| ||||||||||||||| | || |||||||
--tttaatgtcctcatatcatgtgtaagatctctattttctcatttttttaatatgttctgagttggaagagttgacaaatttgctttgaatggttctccagTACTACTTGAAGACAGGAACTTGCAAGTTTGGAGCCACATGCAAGTTTCATCATCCTAGAGACAAGGCTGGAATTGCTGGAAGAGTTTCTTTAAATATTT-
upper sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S102_155V6.1 (Physcomitrella patens), 3'ss of exon 2
--taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaaacattcaccatattacaaatactgattcccttttttgtgc---tttccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
|| || | | | | || | | | | ||| | | | | || | | | | | | | | | | | | ||||| ||||||||||| || |||||||||||||||||||| |||| || |||||||| || || ||||| || | || | || ||||| |
tgatatgcaggagtgggtgtggt--gtccggggtggtgggagttgggaact--agcagcggtggtgctgagggcaggggtggggtgtgtggcgtgagtgtgcagTATTATTTGAAGACGGGGACTTGCAAATTTGGAGCCACGTGCAAGTACCATCATCCGAGGGAGAAGGCGGGATCCACAGGGCGCGTACATTTGAACGTGC-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|254342369|gb|GR858531.1|GR858531EST: AAGGATGAAAGGTGAATTCCCAGAAAGGATAGGACAGCCAGAATGCCAGT ACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATC
genomic: AAGGATGAAAGGTGAATTCCCAGAAAGGATAGGACAGCCAGAATGCCAGGcatgtacttg ... gctttccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttaaacattcaccatattacaaatactgattcccttttttgtgctttccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
tactgat putative branch site (score: 2)
ttcccttttttgtgct CT-rich tract
atattacaaatact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taattttggtcttgatatagtttatatatcatatatgtacttgtgcatttaaacattcaccatattacaaatactgattcccttttttgtgctttccagtACTATTTGAAGACAGGAACTTGCAAATTTGGAGCCACATGCAGGTTTCATCATCCTAGAGACAAGGCTGGGATTGCTGGAAGAGTTGCCTTGAATATTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - -tatgtac
- - - - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaccat