Sequence
atgc intronic sequence ATGC exonic sequencegtatagtttctgttaatgctctttccctccatgtctccctttttttgtgagcatgtggtgtgctttttgtccttattgtgtaagattactatggtgaccttatgcagttggatatgtttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
Basic information
species | Glycine max |
transcript | GLYMA05G32070.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 4
gtatagtttctgttaatgctctttccctccatgtctccctttttttgtgagcatgtggtgtgctttttgtccttattgtgtaagattactatggtgaccttatgcagttggatatgt-ttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
|| || | ||| | | | || | | ||| || || | | || | |||| || ||||| || || || |||||| | |||||||||||||| || || |||||||| ||||| ||||||||||| ||||| ||||| |||||||| ||||||||||
------------------------------------------------------gtactgcacatttgaccagaaaaatcctagtcttggactctgaaattgcttgcttactcttttattctctgcaatg-cagTTAAGCAGCTGTTTCCTTATCTGCATGAAAGATGACAGCATTGAGGGAATCTATGATACTTTGAAGGAATGTGCTGTCATAAGCAAATCTGCTGGAGGAA
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 4
gtatagtttctgttaatgctctttccctccatgtctccctttttttgtgagcatgtggtgtgctttttgtccttattgtgtaagattactatgg--tgaccttatgcagttggatatgtttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
|| | || | | | | | | | ||| ||| || | | || | || | || || ||||| || || || || ||| | |||||||||||||| || || |||||||| ||||| || ||||||||||||| || || |||||||||||||||||||
---------------------------------------------------------gtactgtcttgcttcctgccagacgatgtcattgtgggttgaaattgtttacttactgtttcttttctgtgatg-cagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAGGAGTGTGCTGTAATAAGCAAATCAGCTGGAGGAA
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 4
gtatagtttctgttaatgctctttccctccatgtctccctttttttgtgagcatgtggtgtgctttttgtccttattgtgtaagattactatgg----tgaccttatgcagttggatatg-tttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
|| | || | | | | | | | ||| ||| || | | || || ||| | || || ||||| || || || || ||| | |||||||||||||| || || |||||||| ||||| || |||| |||||||| || || |||||||| ||||||||||
---------------------------------------------------------gtactgtcttgtttcccgccagatgatgtcattgtgggttctgaaattgtttatttactgctgctttttctgtgatg-cagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAAGAGTGTGCTGTAATAAGCAAATCTGCTGGAGGAA
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------gtatagtttctgttaatgctctttccctccatgtctccctttttttg--tgagcatgtggtgtgctttttgtccttattgtgtaagattactatggtgaccttatgcagttgg-atatgtttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
|| | |||| | | || | | | || | | ||||| || ||| || | |||| || | ||| | | || || ||| | || | | | | || || ||| ||||||| ||||||||| | |||||||||||||||||||| || ||||||||||||||| | ||||||||||| || || ||||| || ||||||||||
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttct-tatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatagtttctgtt--aatgctctttccctccatgtctccctttttttgtgagcatgtggtgtgctttttgtccttattgtgtaagattactatggtgaccttatgcagttggatatgtttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
||| || ||| ||| | | ||||| | | |||||| | | || | | ||| || ||| | ||| | | |||| | | ||| | || | | || | ||| |||| |||||||||||||| |||| |||| || || || ||||| || || |||||| ||||||||||||| || |||||||| |||||||| ||||
gtaggacttgcgttccaattcaactggatgccatggttgcaattttttattttattttgttttacttctt-ccctcttggtgggcggt-gtaatggaaggtacttatacctggcttggtgttcgggcgtc--cagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
upper sequence: GLYMA05G32070.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ14283 (Selaginella moellendorffii), 3'ss of exon 4
gtatagtttctgttaatgctctttccctccatgtctccctttttttgtgagcatgtggtgtgctttttgtccttattgtgtaagattactatggtgaccttatgcagttggatatgtttatgtg-cattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
||| || | || | |||| || |||| | | | |||| | | ||| | ||||| ||||||||| | |||||||| || ||||| || || || || ||||| || |||||||||||||||| || ||||| ||||| || || |
--------------------------------------------------------------------------gttg-gttgcttcgtgat--tctccttttgtagttt-acttctaactgtgacttctacagCTTAGTAGCTGCTTCCTTCTCTGCATGAAGGAGGATAGCATTGAAGGCATTTATGATACCCTGAAGGAGTGTGCAGTAATCAGCAAGTCAGCCGGGGGTAMapped 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|193533015|gb|FK493325.1|FK493325EST: TCACTCATGCATCTCCAACACTTTTCAATGCAGGAACACCTAGGCCTCAG TTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATA
genomic: TCACTCATGCATCTCCAACACTTTTCAATGCAGGAACACCTAGGCCTCAGgtatagtttc ... gcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATA
EST:
gi|18040033|gb|BM308327.1|BM308327EST: TCACTCATGCATCTCCAACACTTTTCAATGCAGGAACACCTAGGCCTCAG TTGAGTAGTTGCTTCCTTGTGTGCATG
genomic: TCACTCATGCATCTCCAACACTTTTCAATGCAGGAACACCTAGGCCTCAGgtatagtttc ... gcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaagattactatggtgaccttatgcagttggatatgtttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
atatgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagtttctgttaatgctctttccctccatgtctccctttttttgtgagcatgtggtgtgctttttgtccttattgtgtaagattactatggtgaccttatgcagttggatatgtttatgtgcattggcagTTGAGTAGTTGCTTCCTTGTGTGCATGAAAGATGATAGTATAGAGGGAATATATGACACTTTGAAGGAGTGTGCAGTCATTAGCAAATCAGCTGGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA