Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagttttaaactttttatcttgtgattattccttgtgcttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
Basic information
species | Glycine max |
transcript | GLYMA08G04890.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 13
gtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagttttaaactttttatcttg-tgattattccttgtgcttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
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-----catcaatga--aaatcaagtggatcacatttaaataatgagtcacactgcagtcaggatatgactagctcaccaggatgcttatacctactatgt-tgtttagGTTCTGATCACATTCGTGAGAAAGATGGTATTTGGGCTGTTCTAGCATGGTTATCTATTCTTGCTTTCAAGAACAAGGACAACCTTGGAGGCGATAAGCT
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 13
gtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagttttaaactttttatcttgtgattattccttgtgcttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAG---ACAAGCTTGT
|| ||| | | ||| || | | | || | || || | | || | | || || ||| |||| | | ||| ||| |||| |||||||| ||||||||||||||||| |||||||| || | || ||||| ||||| |||| | || ||||| || || |||| || | |||||
--ttgagttagtggt--catgaatccaacccatagtaaagtcaaggacttgttggtatttggtatagacattattgagatgt--ttatatgtactactt-tggctagGGTCTGACCACATTCGTGAGAAAGATGGCATCTGGGCTGTGCTTGCATGGCTTTCTATTATTGCTTTCAAGAATAAGGACAACCTTGGAGGAGATAAGCT---
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatgtgtttgctattgcattaagaggagcaaa-gtacaactttcaactttattaaaacctagttttaaactttt-tatcttgtgattattccttgtgcttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
||| | | | | |||| | | |||||||| || || | | | || | | |||| | || |||||| || ||||| |||||||||||||| |||||||||||| | || |||||||| ||||| || | || || || || | ||||| | ||
---------------------gtgagcttctattgctagatcttcacatgttttaaaacc--gtaacaaccctacacaactcacaaagaa-------gcttttcgacagGTTCGGATCATATCCGTGAGAAAGATGGGATCTGGGCAGTTCTTGCTTGGCTATCAATACTGGCTCACAAGAACAAGGAAACCCTTGATGGGAATGCAAA
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 14
gtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagttttaaactttttatcttgtgattattccttgtgcttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGA---AGACAAGCTTGT
| | | | ||| | | | ||| | || | || | | | | | | | || | | || ||| || |||| | ||| |||||| ||||| |||||||||||||||||||||||||| ||||| || ||||| ||||| || || ||| ||||||| || || |||| || |||||
-------gtaggtttcatattttgtgtatgaaatt---tctgttaattatgacatacacatatgtaaagcaat--attttg-----atctgttgtatctacggacagGTTCGGACCACATTCGTGAGAAAGATGGAATCTGGGCTGTTTTAGCTTGGCTTTCTATTCTCGCTTATGAAAATAAGGAAAACCTTGGTGGAGCAAAGCT---
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S4_12V6.3 (Physcomitrella patens), 3'ss of exon 14
----------------------------------------------------------------------------gtatgtgtttgctattgcattaagaggagcaaagt-acaactttcaactt---tattaaaacctagttttaaacttttta-tcttgtgattattccttgtgct----tgtgg----atagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
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gtctacgctcattgcatccctcatcgtcaatgccttgcagtttgaaaaagttgtgttggactaatcttattaatggttattctttcatggtttgcttgggttcacgacatttataaactgcgatttatgtacttgagagtagtttaaaaggtttaagtggtgtttttgttttttgaactatggcacggtcttgcagGTTCTGACCACATTAGAGAGAAGGATGGAATTTGGGCCGTTTTGGCATGGCTCTCTATCCTTGCTCACAGGAACAAGCAGGCTGGTGGTGACAAGCTTGTMapped 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|58015854|gb|CX702596.1|CX702596EST: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
EST:
gi|57574755|gb|CX547730.1|CX547730EST: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG GTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
genomic: AATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTGgtatgtgttt ... ttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaacctagttttaaactttttatcttgtgattattccttgtgcttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
ttttaaactttttatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgtttgctattgcattaagaggagcaaagtacaactttcaactttattaaaacctagttttaaactttttatcttgtgattattccttgtgcttgtggatagGTTCTGACCATATTCGTGAGAAAGATGGAATCTGGGCAGTTTTGGCCTGGCTATCTATACTTGCATATAAAAATAAAGATAAACTTGAAGACAAGCTTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT