Sequence
atgc intronic sequence ATGC exonic sequence...tccacttgttggagttcttgttcttcaatcttcctgttgcattgaagtaactataggcatgcgtatttattcagtgatgtactttatgtaatcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
Basic information
species | Glycine max |
transcript | GLYMA11G14770.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
tccacttgttggagttcttgttcttcaatcttcctgttgcattgaagtaactataggcatgcgtatttattcagtgatgtactttatgtaatcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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----------------gtaagttttgcaccttccc-ttgtga-gcaatgcctttaa-----tatccttgttgtttgatct--tttaacttaacttttcagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
upper sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 4
tccacttgttggagttcttgttcttcaatcttcctgttgcattgaagtaactataggcatgcgtatttattcagtgatgtactttatgtaatcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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-------------gtaagttttctgcttcccttcccttgcac----accattctatgc-catatcatggttgcctgaactg-ttaatccatttttca--gCTACATGGGCTGTTTCTGTGTACTTTGCATATCAACGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTATGAGATGGTTAACCACCAGGGCAT
upper sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 4
tccacttgttggagttcttgttcttcaatcttcctgttgcattgaagtaactataggcatgcgtatttattcagtgatgtactttatgtaatcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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-------gtgagttttctccttcccttgccttgcacaccgttcggtgcca-tat---catg---gttgacttgactgagctgttaatcaatttgtttcagCTACATGGGCTGTTTCGGTATACTTCGCGTATCAGCGCACATGGAAGCCTTTTAATCCGATCCTTGGAGAGACTTACGAGATGGTTAACCACCAGGGCAT
upper sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 4
tccacttgttggagttcttgttcttcaatcttcctgttgcatt--gaagtaactataggcatgc---gtatttattcagtgatgtactt-tatgtaatcatc---acagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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-gtaagtattagtatttacacacaaaaaact-cgtattgacttccgactttgtaagatgtatgttaagagttttacttttcttgtggttgtacgtgaatttttatatagCATCATGGGCTATATCTGTTTACTATGCCTTCCAACGAACTTGGAAGCCTTTCAATCCTATTCTTGGGGAGACATATGAGATGGTCAACCATGGTGGGAT
upper sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 4
tccacttgttggagttcttgttcttcaatcttcctgttgcattgaagtaactataggcatgcgt-----atttattcagtgatgtacttt--atgtaatca-tcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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------------------------gtgagtatattcttgcattaaa-tatttcagggcatacatgtattatctggttaatggtggaactttaatgttactaattgcagCATCATGGGCTATATCTGTCTATTATGCCTACCAACGAACTTGGAAGCCTTTTAATCCCATTCTTGGTGAGACTTATGAAATGGCTAATCATGGTGGAAT
upper sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------tccacttgttggagttcttgttcttcaatcttcctgttgcattgaagtaact-ataggcatgcgtatttattcagtgatgtactttatgtaatcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
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gtaagtatcaacatgctgtgtcttgcaataattttttcttacttctgtcaggctgttttatttcatcatttt-tcgtgtaagtgcagttcataagcactt-cgctggagtaataatgaggttcttgt--ttgt-gcagGCACTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATG-----------------Mapped 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|298175652|gb|HO015171.1|HO015171EST: AGATCAAGCAGATGAATCAGAGGATCCATACATGCAGTTAGTTTATGCAA CATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAA
genomic: AGATCAAGCAGATGAATCAGAGGATCCATACATGCAGTTAGTTTATGCAAgtgagttatt ... atcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAA
EST:
gi|18039718|gb|BM308012.1|BM308012EST: AGATCAAGCAGATGAATCAGAGGATCCATACATGCAGTTAGTTTATGCAA CATCATGGGCCATATCG
genomic: AGATCAAGCAGATGAATCAGAGGATCCATACATGCAGTTAGTTTATGCAAgtgagttatt ... atcatcacagCATCATGGGCCATATCG
EST:
gi|151412307|gb|EV282119.1|EV282119EST: AGATCAAGCAGATGAATCAGAGGATCCATACATGCAGTTAGTTTATGCAA CATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTT
genomic: AGATCAAGCAGATGAATCAGAGGATCCATACATGCAGTTAGTTTATGCAAgtgagttatt ... atcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaactataggcatgcgtatttattcagtgatgtactttatgtaatcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
aagtaac putative branch site (score: 2)
tatttattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccacttgttggagttcttgttcttcaatcttcctgttgcattgaagtaactataggcatgcgtatttattcagtgatgtactttatgtaatcatcacagCATCATGGGCCATATCGGTGTACTTTGCGTACCAACGAACCTGGAAGCCTTTTAATCCTATCCTTGGAGAGACTTATGAAATGGTTAACCATGGTGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
-ccacttg
- - - - - - -gttcttg
- - - - - - - - - - - - - - - - -ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgta