Sequence
atgc intronic sequence ATGC exonic sequencegtatcctcatttattttctttttcttttcctatttatcattctctccctttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
Basic information
species | Glycine max |
transcript | GLYMA13G44960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
gtatcctcatttattttctttttcttttcctatttatcattctctccctttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
|||| | |||||||| | | | | | ||| | || | || | | ||| | | ||||||||||||| || || ||||| || ||||| ||||||||||||||||| ||| |||| ||||| ||| ||| ||||| | || ||||| ||||| ||
gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagac--attttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT
upper sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G046480_T01 (Zea mays), 3'ss of exon 4
-----------------------------gtatcctcatttattttctttttcttttcctatttatc--attctctccctttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
| |||| | | | | || || || | | || | ||| || || | | ||| | | || ||||||||||||| || || ||||| ||||| || |||||||| ||||||||||||||||| || ||| || ||| ||||| | || || ||||| || |
gtgtgttctttgctcccatgctgtgctacatttcctaaacaaatattagctttaattaacatctgcttagtacttactatttagtaaagatgtaaaacc--ttttcttttccttctaattgcagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGAGTCGTCCAGCAGTCACT
upper sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
---------gtatcctcat-ttattttctttttcttttcctatttatcattctctccctttgtctgct----------tcgtca--attcaactcacttctgttcatat----ttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
| | ||| | | | |||| | | | | || | |||| | ||| | || | || ||| ||| || || ||| ||||||||| || || ||||| ||||| || |||||||| ||||||||||||||||| || ||| || ||| ||||| |||| || ||||| || |
gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT
upper sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
-------gtatcctcatttattttctttttcttttcctatttatcattctctccctttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
|| | | | |||| || ||| | | | | | ||| | | | | | | || | | || | || ||||||||||||||| || ||||| || || |||||||| || |||||||| || ||||| ||||||||| | |||||||| |||||||||||||| ||
ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT
upper sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S245_10V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------gtatcct-cattt---attttctttttcttttcctatttatcattctctccctttgtctgcttcgtcaattcaactcacttctgtt-catatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
|| | | || | || || || | | | |||| | | | | || | || | || | ||| | | | ||||||||| ||||| || ||||| || || || |||||||||||||||||||| | || || || | ||||||||| | ||||| ||| ||| |
gtatttgctgacgctaaaccctcgcagcattgtgaagcatgttcgatcgaataccttgcaatctgagcttcattcttgtaggaaaacaaaacattttgctgatctagttctctcttgctaaaaagtaacctttgtgacctttgtgcagTTGGAGGTCTCCTGAATGCAACTTTTGGAAATGCAACTGAAATGATTATTTGTATCATGGCCCTGCGGAAGAATATGATACGAGTTGTACAGTTATCACT
upper sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S79_95V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------gtatcctcatttat-tttctt----tttcttttcctatttatcattctctccctttgtctgcttcgtcaattcaactca----cttctgttca-tatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
| || | ||| |||||| | | | | | || | |||| ||| ||| | || | || | || ||||||||||||| ||||| || ||||| || || || |||||||||||| ||||||| | | || | | || |||||| | ||||| || ||| |
gtgattgccgaagttcgaatgttgctgccttatgaagcatattggtttgcatttcttgcaatctgtgctgcagaataggggcaagtgtgtttggctgattcaattctctgacgaagaaactgatctttgctatttgcagTTGGAGGTCTCCTGAATGCGACCTTTGGAAATGCAACTGAAGTGATTATTTGTGTCATGGCTCTCCGGAAGAACATGATACGAGTTGTACAATTATCACT
upper sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
gtatcctcatttattttctttttct-------tttcctatttatcattctctccc-tttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
|| | | || || | | | | ||| ||| |||| | | ||| || || | | || | |||||||||| ||||| || ||||| || || ||||||||||| ||||||||||||| || ||| || | || |||||| | ||||| ||| ||| |
-taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACTMapped 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|10848150|gb|BF070698.1|BF070698EST: GCAGCTTGCCTTCTACACAGGACCCACAG TTGGGGGTCTGCTTAATGCCACATTCNGCAATGCAACTGAAATGATGATAT
genomic: GCAGCTTGCCTTCTACACAGGACCCACAGgtatcctcat ... atatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATAT
EST:
gi|8670423|gb|BE191530.1|BE191530EST: GCAGCTTGCCTTCTACACAGGACCCACAG TNTGGGG-TCTGCTTAATGCCACATTCGGCAATGCAACTGAAATG
genomic: GCAGCTTGCCTTCTACACAGGACCCACAGgtatcctcat ... atatttgcagT-TGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctctccctttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
aactcac putative branch site (score: 2)
ttcatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcctcatttattttctttttcttttcctatttatcattctctccctttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA