Sequence
atgc intronic sequence ATGC exonic sequencetgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattgcatggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA
Basic information
species | Glycine max |
transcript | GLYMA18G39880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattg--catggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA-
| | | | | ||| | ||| | | | | || ||||||||| | ||| ||| |||| ||| | |||| |||||| ||| || || || || |||||||| |||||||| || ||||| ||||| ||||| ||||||||||| || |
-----------------------------gtaagttttgcaccttcccttgtgagcaatgcctttaatatccttgttgtttgatcttttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
upper sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 4
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattgcatggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA-
| | ||| || | | ||||| | | ||| | | | ||| |||| || | | | | | |||| |||| ||| | | || | |||| ||| |||||||| ||||||||||| || ||||| || ||||| ||||||||||| ||||||||||| ||||
-------------gtaagttttctgcttcccttcccttgcacaccattctatgccatat-catg-gttgcctgaactgttaatcca--------tttttcagCTACATGGGCTGTTTCTGTGTACTTTGCATATCAACGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTATGAGATGGTTAACCACCAGGGCAT
upper sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattgcatggaat--ttgatcttacagattattt-ttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA-
| | ||||| ||||| | || | | || || |||| || || | ||| || | |||| || |||| ||| | | || | |||| || ||||| || ||||||||||| || ||||| || ||||| |||||||| || ||||||||||| ||||
------------------gtgagttttctccttcccttgccttgcacaccgttcggtgc-catatcatggttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
upper sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g00480.t01 (Vitis vinifera), 3'ss of exon 4
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattgcatggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA-
|| | |||| || ||||| ||| || | || | || || ||| | | |||||||||||| |||||| || || || |||| |||||| || |||||||| || ||||||||||||||||||||||||||| || || ||||||||||
------------------------gtaagcgttcccc---ttctatctct-ctattgaattatccgtt--------ctggacctcacacttgtctgttgcagCATCATGGGCTATATCAATGTATTACGCCTGTCAACGTACCTGGAAGCCTTTTAATCCAATTCTTGGTGAGACTTATGAATTGACCAATCATGGTGGCAT
upper sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------tgtaagcattactt-tcacattt------ttgttctctctccctcgtctccgtctc--tgtcatttgtgcatacattgcatggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA
|| || ||| || | || | | |||| | | || | | ||| | || || | || | || |||| | | || ||| ||||| | | | || | || || |||||| | ||||||||||| |||||||| ||||| || |||||||||||||||
gtaagtatcaacatgctgtgtcttgcaataattttttcttacttctgtcaggctgttttatttcatcatttttcgtgtaagtgcagttcataagcacttcgc-tggagtaataatgaggttcttgtttgtgcagGCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATG----------------
upper sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 4
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattgcatggaat-ttgatctt-acagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA-
|| | | ||| || | | ||| | |||| | | || || | |||| | | ||| || | || ||||| || |||| | ||||||||||||||||| ||||| || ||||| ||||||||||| || ||| ||||||
--------------------------------------------------gtaagtggtgaattctctttctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAACGTGCGTGGAAGCCATTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCAT
upper sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 4
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattgcatggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA-
|| | || || || || | || | | || || | |||| | | ||| || | || ||||| || | || | |||||||| |||||||| ||||| || ||||| ||||||||||| || ||| ||||||
--------------------------------------gtaagtggtgaattctctttctttctcagcctggggtgctgattcggattgttttcttctacagCGTGCTGGGCTATCTCTGTATATTATGCTTACGAGCGGCCGTGGAAGCCTTTCAATCCTATTCTCGGGGAGACGTATGAAATGGTGAATCATAGTGGCATMapped 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|254320166|gb|GR829354.1|GR829354EST: TAGATATGGCAGATAAGACTGAGGATCCATACATGAGACTAGTATATGCT TCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCA
genomic: TAGATATGGCAGATAAGACTGAGGATCCATACATGAGACTAGTATATGCTtgtaagcatt ... tatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCA
EST:
gi|254346587|gb|GR856309.1|GR856309EST: TAGATATGGCAGATAAGACTGAGGATCCATACATGAGACTAGTATATGCT TCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCA
genomic: TAGATATGGCAGATAAGACTGAGGATCCATACATGAGACTAGTATATGCTtgtaagcatt ... tatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctgtcatttgtgcatacattgcatggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA
atcttac putative branch site (score: 3)
ttattttt putative PPT
ttacagattattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtaagcattactttcacatttttgttctctctccctcgtctccgtctctgtcatttgtgcatacattgcatggaatttgatcttacagattatttttgcaGCATCATTCTTTATATCCATCTACTATGCCTATCAACGAACATGGAAGCCATTCAATCCAATTCTTGGTGAGACTTATGAAATGGTTAACCATGGTGGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG