Sequence
atgc intronic sequence ATGC exonic sequencegtatagccttatctttgtgcttctttcccctccattgtttaccctgatatacttaatcttttgttatacacctttgtgtcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACTAGATCTAAGTAAACAGCCTCCTGCCGTTCGATTAAACAAGGAACTGGAT
Basic information
species | Glycine max |
transcript | GLYMA05G29330.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 12
-------------------------gtatagccttatctttgtgctt---ctttcccctccattgtttaccctgatatacttaatcttt--tgttatacacctttgtgtcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACTAGATCTAAGTAAACAGCCTCCTGCCGTTCGATTAAACAAGGAACTGGAT
||| | | ||| | | | | || | || || | | || | | ||| | | || | |||||||| ||||| || || ||||||||||||||||| || || || || || ||| |||||||||| |||||||| ||||| | ||||| || ||||
gtttgttctttgtactagttttactatatgacatcatcagaataaatgagcactgtaatcgtccgattgtttggaagtcatcaagactcactagaataaatgacaattctacttgcagGTTTGTCCATGTTAGTTCTGCAGGAGTTACAAGACCTGAGAGACCAGGCCTGGATTTAAGTAAACAACCTCCTGCTGTTCGCATGAACAAAGAGCTGGGC
upper sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G019358_T01 (Zea mays), 3'ss of exon 12
------gtatagccttatctttgtgcttctttcccctccattgttt----accctgatatacttaatc---ttttgttatac--acctttgtgtcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACTAGATCTAAGTAAACAGCCTCCTGCCGTTCGATTAAACAAGGAACTGGAT
||| | | | | | | || || |||| ||| | | || | |||| | | | | ||| | | | || ||||| || |||||||| || || |||||||||||||| ||||| || || ||||| |||| || ||||| ||||| |||||||| ||||| || || |
gcaatgacataagtaaaacagaatacatatagccacttcattttttcagtttctttatggaaccaatcaggactgactgggcttgcttttcttttatatgaagGTTCGTTCATGTGAGTTCTGCGGGAGTTACAAGACCTGAAAGACCGGGGTTAGATTTAAGCAAGCAGCCACCTGCTGTTCGATTGAACAAAGAGCTTGGC
upper sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G019358_T02 (Zea mays), 3'ss of exon 12
------------------------------gtatagccttatctttgtgcttctttcccctccattgttta----ccctgatatacttaatct---tttgttatac--acctttgtgtcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACTAGATCTAAGTAAACAGCCTCCTGCCGTTCGATTAAACAAGGAACTGGAT
||| | | | | | | || || |||| ||| | | || | |||| | | | | ||| | | | || ||||| || |||||||| || || |||||||||||||| ||||| || || ||||| |||| || ||||| ||||| |||||||| ||||| || || |
gtttgtctatctgctagttttcaggcaatgacataagtaaaacagaatacatatagccacttcattttttcagtttctttatggaaccaatcaggactgactgggcttgcttttcttttatatgaagGTTCGTTCATGTGAGTTCTGCGGGAGTTACAAGACCTGAAAGACCGGGGTTAGATTTAAGCAAGCAGCCACCTGCTGTTCGATTGAACAAAGAGCTTGGC
upper sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 12
------------------------------------------gtatagccttatctt-tgtgcttctttcccctccattgtttaccctgatatacttaatcttttgttatacacctttgtgtcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACTAGATCTAAGTAAACAGCCTCCTGCCGTTCGATTAAACAAGGAACTGGAT
|| | || || |||||| | || | | | || | || | || | | ||| ||| | ||||||||||||||||||||| || ||||| || |||| || ||||| ||||| || || ||||||||||||||||| ||||| || ||||||||| |||
gtttaatattccttctcattttgctaaaattagtccatacacacatttctgtagtttatgtgctggaaagcaggttatcttcttgagtcatgttctgctttccttatcttttgaagttgctccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACTTGACCTTAGTAAACAGCCTCCTGCTGTTCGCTTGAACAAGGAATTGGGCMapped 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|22522381|gb|BU081192.1|BU081192EST: CCAGTGTCTAGCATACATGCATATATAATAAAGGATCCAATAACCCCCAG GTTTGTACATGTGAGCTCAGCAAGAGTTACAAGACCCGAAAGGCCTGGACT
genomic: CCAGTGTCTAGCATACATGCATATATAATAAAGGATCCAATAACCCCCAGgtatagcctt ... tcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtttaccctgatatacttaatcttttgttatacacctttgtgtcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACTAGATCTAAGTAAACAGCCTCCTGCCGTTCGATTAAACAAGGAACTGGAT
acttaat putative branch site (score: 4)
atatacttaatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagccttatctttgtgcttctttcccctccattgtttaccctgatatacttaatcttttgttatacacctttgtgtcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACTAGATCTAAGTAAACAGCCTCCTGCCGTTCGATTAAACAAGGAACTGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA