Sequence
atgc intronic sequence ATGC exonic sequencegtaaccaactcccttctcgacattttcttttacttttttatgtataacgataattctctcaatcagatttcttttttttccagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAA
Basic information
species | Glycine max |
transcript | GLYMA14G00540.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G00540.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g03270.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaaccaactcccttctcgacattttcttttacttttttatgtat-------aacgataattctctcaatcagatt--tcttttttttccagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAA
| | ||| | | ||| | | | ||| ||||| | || || ||| | ||| | | || |||||||||||| ||||||||||| |||||||||||||| || || ||| | || || || ||||| ||||| ||||| || |||||
tagtaaggactattatttccttgttttggattgcatgatcaatctttctgtatcttttggacttgtactttctgtaattgctataatctgtatattgtagGAAGGGTCACCCCTGAAAGTGTTATTTACAGCTTTGGTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCAT
upper sequence: GLYMA14G00540.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------gtaaccaactcccttctcgacattttcttttacttt-------tttatgtataacg-----ataattctctcaat-------cagatttcttttt----tttccagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAA
| | |||| | || ||||| ||| || | ||| |||| | || |||||| || || || | ||| |||| ||||| ||||||||||||||||||||||||| ||||| ||||| || || | | ||||| ||||| || ||||| || |||
gtatcccacggtttccctctttctggatcgaatatttgagcaacctggaaattagcaatttctattatgttaaatgtatgcatgcataatgtatgcatgcttctctttggtacgtgacaaatgtcataagagggtttgcagGGAGGGTGACGCCTGAAAGTGTCATTTACAGCTACGGAACGGTTCTGCTGGATTTGTTGAGTGGGAAGCATATACCTCCTAGCCAA
upper sequence: GLYMA14G00540.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------gtaaccaactcccttc-tcgacattttcttttacttttttatgtataacgataattctctcaatcagatttcttttttttccagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAA
| | || || | |||| || ||| | | | | | ||| |||| | |||| |||||||||| || |||||||||||||||||||||| ||||| ||| | ||||| | | ||||| |||||||| |||||||| ||
gttaacaactttttgggcatcttctgggaagagcttgtgagggaatggtgggttagctatatttttgtcttcgtaagatcgatgttcactgcctaagtcaatcggtcgaggaaccctggaactcccgtgattctgtttg-gtcagtgacggtcatttttcgatattttgcagGAAGGGTAACTCCTGAAAGTGTCATTTACAGCTACGGAACTGTTTTACTAGATTTGTTGAGTGGGAAGCACATACCTCCCAGCCAT
upper sequence: GLYMA14G00540.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S178_86V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------------------------------gtaaccaactccc--ttctcgacatttt------cttttacttttttatgtataacgataattctctcaatcagatttcttttttttccagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAA
||| || | || | ||||| | | ||| |||| || |||| || | | ||| |||| ||||| || ||||||||||| |||||||||| |||||| ||||| ||||| || | ||||| ||||| | ||||| |||||
gtaccaacttggcatacacccccccatgagtacttaagaactggtaacgaagtctgaagcttggtaatgtatttgcgcaattctggacattattacggacctacccaaaattaccaacattcaaagcagccctggatttagtatgcttactttggattcctgagattcttgtattcaaatttgcagGTAGGGTGACACCTGAAAGTGTTATTTACAGCTATGGAACTGTTCTACTAGATCTGTTGAGTGGGAAGCATCTACCTCCTAGTCACMapped 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|193657600|gb|FK606765.1|FK606765EST: GAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGAAATG GAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAG
genomic: GAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGAAATGgtaaccaact ... ttttttccagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAG
EST:
gi|298184099|gb|HO029312.1|HO029312EST: GAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGGAATG GAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAG
genomic: GAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGAAATGgtaaccaact ... ttttttccagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacttttttatgtataacgataattctctcaatcagatttcttttttttccagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAA
gtataac putative branch site (score: 3)
tttcttttttttcc putative PPT
ttttttatgtataacg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaccaactcccttctcgacattttcttttacttttttatgtataacgataattctctcaatcagatttcttttttttccagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC