Sequence
atgc intronic sequence ATGC exonic sequence...gtttataatttccttgacttgtgctttttgtttctttgtttatactttttctggtcttgtacttccattggtaccttactggttttaattttattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
Basic information
species | Glycine max |
transcript | GLYMA07G00350.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 7
gtttataatttccttgacttgtgctttttgtttctttgtttatactttt----tctg-gtcttgtacttccattggtaccttactggttttaattttattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
| | || || |||| | || | | |||| || || |||| | | | ||| ||| |||| | || | |||||||||||||||| ||||||||||| || ||||| ||||| |||||||| || || ||||||||||| |||||||| |||||||| || ||||||||||
--agagatgcatctcgaaaatcactttgtattattattattatcctattatgctctgtaacacatgtatacatcagtagtatactaaaag-agggctactc--agGTTGGTGACAATGTTGGAGATTGTGCCGCACGAGGGGCTGACCTTTTTGAGAGCATAGCAGCTGAAATTATCAGTGCAATGATACTCGGGGGAACAATGG
upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 7
gtttataatttccttgacttgtgctttttgtttctttgtt-----tatactttttctggtcttgtacttccattggtaccttactggttttaattttattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
| ||||| ||| | ||| || | ||||| ||| || | | |||| | || | || | ||| || | | |||||||||||||||| |||||||||||||| ||||| |||||||||||||| || || ||||| ||||| |||||||| ||||||||||| ||||||||||
----aatatttctttgctctacaactttacttgccttgttcttgttatcctatagttcatcttttgctactatatat-tcttgtataacaaaagaaactactcagGTTGGTGACAATGTTGGAGATTGTGCTGCCCGAGGCGCTGATCTTTTTGAGAGCATAGCAGCAGAAATTATCAGTGCAATGATACTTGGAGGAACAATGG
upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G78920.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------------gtttataatttccttgact-tgtgctttttg-------tttctttgttta----------tactttttctggtcttgtacttccattggtaccttactggttttaa-----ttttatttta----agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
|||| | | || ||||| | |||| || || |||||| ||| | || ||| | || || ||| ||| || ||| || || ||||||| ||||||||||| || ||||||||| ||||||||||| | ||||||||||| || || ||||| |||||||| |||||||| |||||||||||||
gtatttgatctttgttctttttgtttcttactttcttgattctgtgattcccaaacgtgacatccttgtttggggcatatatcactctacaagggtttgcttgtgttttcgtcatttaggcatttaaagccattttcatcttcttgtagGTTGGAGACAATGTGGGGGACTGTGCTGCTAGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTAGGTGGAACAATGG
upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 8
gtttataatttccttgacttgtgctttttgtttctttgtttatactttttctggtcttgtacttccattggtaccttactggttttaattttatttta----agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
||| | ||| || | | | | | |||||| ||| |||| || | || | | ||| | | | || | | | || || ||||||| |||||||| || || || |||||||||||||||||| | ||||||||||| || || ||||| |||||||| ||||||||||| || |||||||
--gtattagttctttcatt------tcacgatcctttgtgtatgattttgtcgggcctggaac-cttttgtcatcactgaagcttcactctcatcttcttgcagGTTGGAGACAATGTTGGGGACTGCGCTGCTCGAGGTGCTGATTTATTTGAAAGTATAGCTGCAGAAATCATCAGTGCAATGATACTTGGGGGTACAATGG
upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 7
gtttataatttccttgacttgtgc--tttttgtttctttgtttatactttttctggt-----cttgtacttccattggtaccttactggttttaattttattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
|||| || | | |||| |||| | |||||| | | | | | ||| ||| | | | | | || |||| |||||||| |||||||| || |||||||||||| ||||||||||||| ||||||||||||||||||||||| |||||||| |||||||| |||||||||||||
-------atttgtttcattggtgcatttttcatgtctttgccttttttctaagggaaaaatgtatgtcctttccataacaagagttttccctcttcttcatttgaagGTTGGAGACAATGTTGGTGATTGTGCTGCTAGAGGTGCTGATCTGTTTGAAAGTATTGCAGCTGAAATCATCAGTGCTATGATACTGGGTGGAACAATGG
upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------gtttataatttccttgacttgtgctttttgtt---tctttgtttatact-----------ttttctgg---tcttgtacttccattggtaccttactggttttaattt-tatttta----agGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
|| | | ||| ||| | || || | || ||| | || | | ||| | | | |||| || ||||| | | | || | | || || |||| || ||||| ||||||||||||||||| || ||||| ||| | ||||||||||||||||||||||| |||||||||||||| |||||||| || ||||
gtatgtgtaaatgcgttcttttctgtatctgtaagtgtctagtcgtgtctgttttacttcagcgttggttctagtcctctctatacttgcaatgtcaaatagaatttattaaaaatttagtacgtctattggcagtccagttattgaagcctgtacattggagcagGTCGGAGACAACGTGGGAGATTGTGCTGCCCGTGGTGCGGATTTATTTGAAAGTATTGCAGCTGAAATTATCAGTGCCATGATTCTTGGTGGCACCATGG
upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S28_200V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------gttta---taatttccttgacttgtgc---tttttgtttctttgtt-----tatactttttctggtcttg--tacttccattggtaccttactggttt-taattttattttaa----gGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
|| || | || | |||| ||| || | || | || | || | || || ||| ||| || |||||| | | | | | | || | | ||||||||| || ||||||||||||||||| || ||||| ||| | ||||||||||||||||||||||| |||||||||||||| |||||||| |||||||
gtatgctcaaattaatgttattctgtatatgtagttgtctaattttgattattagactggtgtcagttgtagtgtgttggacactagtagagttcatccacatttgagtacctctattggtcttccagttgctgatgcctgtacatcgaagtagGTTGGTGATAACGTGGGAGATTGTGCTGCCCGTGGTGCCGATTTATTTGAAAGTATTGCAGCTGAAATCATCAGTGCCATGATTCTTGGTGGTACAATGG
upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ13082 (Selaginella moellendorffii), 3'ss of exon 6
gtttataatttccttgacttgtgctttttgtttctttgtttatactttttctggtcttgtacttccattggtaccttactggttttaattttattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
| ||||| || | | || ||| ||||| | || ||||||| || ||||| || |||||||||||||| ||||||||| | || ||||||||||| || || ||||| || |||||||| || || || || ||||
-------------------------------------------------gtaaattttgtagttta--cgtttagttgatggacttaatggt-cttacagGTTGGAGATAATGTTGGTGATTGTGCTGCTCGTGGTGCTGATTTATTCGAAAGTATTGCTGCGGAGATAATTAGCGCCATGATTCTGGGAGGCACTATGGMapped 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|193482825|gb|FK447042.1|FK447042EST: AGGGAATACCTGAAGATGACCCTAGGAATCCTGCTGTTATTGCTGATCTG GTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATTCTTTTTGA
genomic: AGGGAATACCTGAAGATGACCCTAGGAATCCTGCTGTTATTGCTGATCTGgtaattgttt ... ttattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGAT-CTTTTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttctggtcttgtacttccattggtaccttactggttttaattttattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
ttttaat putative branch site (score: 3)
ttttatttt CT-rich tract
ttactggttttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttataatttccttgacttgtgctttttgtttctttgtttatactttttctggtcttgtacttccattggtaccttactggttttaattttattttaagGTTGGTGACAATGTGGGAGATTGTGCTGCTCGAGGTGCTGATCTTTTTGAAAGTATTGCAGCTGAAATAATCAGTGCCATGATACTTGGTGGAACAATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - -ttccttg
- - - - - - - - -cttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttactg