Sequence
atgc intronic sequence ATGC exonic sequence...tttagtttactgggaatcgtagattgagaattttcgtttcccatgtttggtatcaattttttaaaaataacattcccgatgttttgttttgttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCTCTTATGTCTGGTGGGCAGCCAA
Basic information
species | Glycine max |
transcript | GLYMA02G13780.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G13780.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 3'ss of exon 4
tttagtttactgggaatcgtagattgagaattttcgtttccca-tgtttggtatcaattttttaaaaat--aacattcccgatgttttgttttgttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCTCTTATGTCTGGTGGGCAGCCAA
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----gtatgatctcaatatttctctcaagaccacattcacataatgtacagtattgattttcctagtatttagtgtgctcattgatttgtttt-ctatc--agGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGCTGTGATAAACAAGTAAAAATGTGGCCTCTGTTGTCTGGTGGGCAGGCTC
upper sequence: GLYMA02G13780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G058498_T01 (Zea mays), 3'ss of exon 4
-------tttagt--ttactgggaatcgtagattgagaattttcgtttcccat--gtttggtatcaattt--tttaaaaataacattcccgatgttttgttttgttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCTCTTATGTCTGGTGGGCAGCCAA
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gtatgatcttagtgttttctggga----tatgttaatatatttgattgggcggtagattgtcttccatgtagtttgtatctggtatcctcattgatttgtttcctttt---agGTTCTCTGCTCGGCTTGGAAGGATGATGGAACTACTGTCTTCTCTGGAGGCTGTGACAAGCAGGTCAAAATGTGGCCTCTTCTGTCAGGTGGGCAGCCTC
upper sequence: GLYMA02G13780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G180815_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------tttag--tttactgggaatcgtagattgagaattttcgtttcccatgtttggtatcaattttttaaaaataacattcccgatgttttgttttgttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCTCTTATGTCTGGTGGGCAGCCAA
|||| ||| || | | | |||| | || | | || |||| | | | | | | ||| | | |||||||| || | |||| ||||||| ||||||||||| ||||| ||| ||||| || || |||||||| |||||||| || |||||||| || | || |||| ||||| |
gtattgtgattgtcttagcacttttttcacccagaagtgattcgtcttagcatttgctcatattagctgattatggatctagatgtctt-tgttctaggccctctgtatgcgactcacaggctgg---ttttgtttcgt----gcagGTGCTGTGCTCGGCTTGGAAGGATGATGGGTTGACTGTTTTCTCAGGAGGCTGTGATAAGCAGGTTAAAATGTGGCCCCTGCTCTCAGGTGCCCAGCCCA
upper sequence: GLYMA02G13780.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ10886 (Selaginella moellendorffii), 3'ss of exon 3
--------tttagtttactgggaatcgtagattgagaattttc----gtttcccatgtttgg-tatcaattt--tttaaaaataacattcccgatgttttgttttgttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCTCTTATGTCTGGTGGGCAGCCAA
|||| | | || ||| ||| || | |||| || | |||| ||| || | | | | | | ||| | ||| || | |||| |||||||| ||||||||||| ||||| ||||| || || || || || || || || ||||||||||||||||||||| || || ||| ||
gtaagtcttttacatgctcgaaaaaaaaggatctagacttgttctaagtttttcaagattggatatttccttggctcgagagctaagctttct---tttcgcttttttctc--agGTATTGTGCTCGGCTTGGAAGGATGATGGCACGACTGTCTTCTCAGGAGGATGCGATAAACAGGTCAAGATGTGGCCTCTTTCATCCGGAAACCAGTCAG
upper sequence: GLYMA02G13780.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ25923 (Selaginella moellendorffii), 3'ss of exon 3
--------tttagtttactgggaatcgtagattgagaattttc----gtttcccatgtttggtatcaattttttaaaaataacattcccgatgttttgttttgttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCTCTTATGTCTGGTGGGCAGCCAA
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gtaagtcttttacatgctcgaaaaaaaaggatctagacttgttctaagtttttcaagattggatttttccttgactcgagagctaagctttcttttcgcttttttctc--agGTATTGTGCTCGGCTTGGAAGGATGATGGCACGACTGTCTTCTCAGGAGGATGCGATAAACAGGTCAAGATGTGGCCTCTTTCATCCGGAAATCAGTCAGMapped 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|37996246|gb|CF807835.1|CF807835EST: GGACTGTTGTCAACAGCACTCCCAAGGCTTCCATTTCTCACGACCAACCG GTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGC
genomic: GGACTGTTGTCAACAGCACTCCCAAGGCTTCCATTTCTCACGACCAACCGgtaatgaaat ... gttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGC
EST:
gi|151398315|gb|EV268186.1|EV268186EST: GGACTGTTGTCAACAGCACTCCCAAGGCTTCCATTTCTCACGACCAACCG GTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGC
genomic: GGACTGTTGTCAACAGCACTCCCAAGGCTTCCATTTCTCACGACCAACCGgtaatgaaat ... gttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggtatcaattttttaaaaataacattcccgatgttttgttttgttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCTCTTATGTCTGGTGGGCAGCCAA
aaataac putative branch site (score: 2)
ttttgtt putative PPT
tatcaattttttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttagtttactgggaatcgtagattgagaattttcgtttcccatgtttggtatcaattttttaaaaataacattcccgatgttttgttttgttgttgaagGTTTTGTGCTCCGCTTGGAAGGACGATGGAACGACAGTTTTTTCTGGGGGCTGTGACAAGCAGGTCAAGATGTGGCCTCTTATGTCTGGTGGGCAGCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - ttactgg
- - - - - - - - - - - - - - - - - - - - ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattccc