Sequence
atgc intronic sequence ATGC exonic sequencegtaactaactcccttctcgacatttactttttatatataatataataactcgtttctctcaatcggaatgcttttgttacagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAT
Basic information
species | Glycine max |
transcript | GLYMA02G48030.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G48030.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g03270.t01 (Vitis vinifera), 3'ss of exon 4
--------gtaactaactcccttctcgacatt-------tactttttatatataatataataactcgtttctctcaatcggaatgcttt---tgttacagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAT
| || ||| | | ||| | | ||| | ||| | | || ||| | || | | | || |||||||||||| ||||||||||| |||||||||||||| || || ||| | || || || ||||| ||||| ||||| || ||||||
tagtaaggactattatttccttgttttggattgcatgatcaatctttctgtatcttttggacttgtactttctgtaattgctataatctgtatattgtagGAAGGGTCACCCCTGAAAGTGTTATTTACAGCTTTGGTACTGTCCTTTTGGATCTGCTAAGTGGAAAGCATATCCCGCCAAGTCAT
upper sequence: GLYMA02G48030.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------gtaactaactcccttctcgacatttactttttatat--ataatataataactcgtttctctcaatcg----gaatgcttttg------ttacagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAT
| || || | | | || | | | | || ||||| || | | | ||| | || |||| | || |||| ||||| ||||||||||||||||||||||||| ||||| ||||| || || | | ||||| ||||| || ||||| || ||
gtatcccacggtttccctctttctggatcgaatatttgagcaacctggaaattagcaatttctattatgttaaatgtatgcatgcataatgtatgcatgcttctctttggtacgtgacaaatgtcataagagggtttgcagGGAGGGTGACGCCTGAAAGTGTCATTTACAGCTACGGAACGGTTCTGCTGGATTTGTTGAGTGGGAAGCATATACCTCCTAGCCAA
upper sequence: GLYMA02G48030.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S9_348V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------------gtaactaactcccttc-tcga-catttactttttatatataatataataactcgtttctctcaatcggaatgcttttg-------ttacagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAT
| | ||| ||| || | | | | | | | || || ||| | | |||| || |||||||||| || |||||||||||||||||||||| ||||| ||| | ||||| | | ||||| |||||||| |||||||| |||
gttaacaactttttgggcatcttctgggaagagcttgtgagggaatggtgggttagctatatttttgtcttcgtaagatcgatgttcactgcctaagtcaatcggtcgaggaaccctggaactcccgtgattctgtttggtcagtgacggtcatttttcgatattttgcagGAAGGGTAACTCCTGAAAGTGTCATTTACAGCTACGGAACTGTTTTACTAGATTTGTTGAGTGGGAAGCACATACCTCCCAGCCAT
upper sequence: GLYMA02G48030.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S178_86V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------------gtaactaactccc-ttctcgacatttact----ttttatatataatataataactc--gtttctctcaatcggaatgcttttgtt-acagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAT
| | ||| | || | ||||| | | || || ||| | ||| | ||| || | | || |||| ||||| || ||||||||||| |||||||||| |||||| ||||| ||||| || | ||||| ||||| | ||||| |||||
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|254344188|gb|GR855273.1|GR855273EST: GAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGAAACG GAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAG
genomic: GAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGAAACGgtaactaact ... tttgttacagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAG
EST:
gi|16347764|gb|BI973359.1|BI973359EST: GAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGAAACG GAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAG
genomic: GAGTTATAGCACCAATCTTGCTTACACACCTCCTGAATATTTAAGAAACGgtaactaact ... tttgttacagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttatatataatataataactcgtttctctcaatcggaatgcttttgttacagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAT
taataac putative branch site (score: 1)
cttttgtt putative PPT
atatataatataataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactaactcccttctcgacatttactttttatatataatataataactcgtttctctcaatcggaatgcttttgttacagGAAGGGTCACGCCTGAAAGTGTCATTTACAGCTTTGGAACCGTTCTTCTAGACCTCCTCAGTGGCAAGCACATCCCTCCCAGTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC