Sequence
atgc intronic sequence ATGC exonic sequence...aagtgttgagcttgaacatcttttttttttttgcacttaaaaaatctttaagtttttctagtcttgagtcttgactatcgaactttgaaaataaatgtagGAGGATGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAGTCTGGGTGCCTCAAGAAGTATTGTGAATGCTTCCAAGCCA
Basic information
species | Glycine max |
transcript | GLYMA07G09380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G09380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
-----aagtgttgagcttgaacatcttttttttttttgcacttaaaaaatctttaagtttttctagtcttgagtcttgactatcgaactttgaaaataaatgtagGAGGATGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAGTCTGGGTGCCTCAAGAAGTATTGTGAATGCTTCCAAGCCA
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ctatcaaatactgaaatt--atgtcattattgcatttaatttggaccaagttattgtgctgccatgacatgtggcattaattctagtccatgaaattgc---tagGAGGTGTCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: GLYMA07G09380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
---aagtgttgagcttgaacatcttttttttttttgcacttaaaaaatctttaagtttt-tctagtcttgagtcttgactatcgaactttgaaaataaatgtagGAGGATGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAGTCTGGGTGCCTCAAGAAGTATTGTGAATGCTTCCAAGCCA
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atcaattacaggcatt--atatcattattgcattt-catttcggccatgttattgtgctgccttgacacgtcacattaattctagtccatgaaattttgc-cagGAGGTGCCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: GLYMA07G09380.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
------aagtgttg-agcttgaacatcttttttttttttgcacttaaaaaatctttaagtttttctagtcttgagtcttgactatcgaactttgaaaataaatgtagGAGGATGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAGTCTGGGTGCCTCAAGAAGTATTGTGAATGCTTCCAAGCCA
| | || || || | || |||||| || || | || | | | | | || | | | | ||||||| || | || ||||||||||||| || | | | || ||||| ||||| || |||||||| || || || |||||||||||||||||||| |||||||||||||| |
tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaa---tagaacttt----attattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
upper sequence: GLYMA07G09380.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 5
aagtgttgagcttgaacatcttttttttttttgcacttaaaaaatctttaagtttttctagtcttgagtcttgactatcgaactt--tgaaa-----ataaatgtagGAGGATGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAGTCTGGGTGCCTCAAGAAGTATTGTGAATGCTTCCAAGCCA
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------cgtattccttc-tgttgtaccaaattatattccatagtttcattatttttcttaacctgggcgagtggttgacgaaactgatggcatcttggttattgcagGAGGATGTTGGAGAGCATCCTCTGGCGGGCAAGCACAACAAAGGATGCCACTGTAAAAAGTCGGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCCAMapped 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|193523498|gb|FK478317.1|FK478317EST: CATTTAGGCCCAAAATTGCTAGCAGTCCTCATGGAACACGTGATAGCAGG GAGGAGGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCAT
genomic: CATTTAGGCCCAAGATTGCTAGCAGTCCTCATGGAACACGTGATAGTAGGgtactcggtt ... ataaatgtagGAGGATGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttaagtttttctagtcttgagtcttgactatcgaactttgaaaataaatgtagGAGGATGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAGTCTGGGTGCCTCAAGAAGTATTGTGAATGCTTCCAAGCCA
tcttgac putative branch site (score: 3)
aactttgaaaataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagtgttgagcttgaacatcttttttttttttgcacttaaaaaatctttaagtttttctagtcttgagtcttgactatcgaactttgaaaataaatgtagGAGGATGCTGGGGAAGTTTTAATATTAGGAAAACATAACAAGGGGTGTCATTGTAAAAAGTCTGGGTGCCTCAAGAAGTATTGTGAATGCTTCCAAGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- -tgttgag
- - - - - cttgaac
- - - - - - - - - - - - - - - -tgcactt
- - - - - - - - - - - - - - - - - - - aaaaaat