Sequence
atgc intronic sequence ATGC exonic sequencegtaagattttctactacatcacttgcatgggagaaatatagttctttaatttcagtgattgcaattgcattcatctgttatgcagttttggtaatatgccttaaattttaaattccatacagGTCACGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAAATTTTTGACAGATGCCAAATTGGCTATAA
Basic information
species | Glycine max |
transcript | GLYMA14G31890.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G31890.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 3
gtaagattttctactacatcacttgcatgggagaaatatagttctttaatttcagtgattgcaattgcattcatctgttatgcagttttggtaatatgccttaaattttaaattccatacagGTCACGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAAATTTTTGACAGATGCCAAATTGGCTATAA
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-------------------------------------------------gttggaaaattttccttcagacctcttgttgtctatcagttgttctattttaaacgtttcttttctgttgcagGTCATGGTGGTTCACGTGCTGCTGAGTATTTGAAGGAGCACTTGTTTGAGAACCTCATGAAACATCCAGAGTTCATGACAAATACAAAATTAGCAATAA
upper sequence: GLYMA14G31890.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G412937_T01 (Zea mays), 3'ss of exon 3
gtaagattttctactacatcacttgcatgggagaaatatagttctttaatttcagtgattgcaattgcattcatctgttatgcagttttggta-atatgccttaaattttaaattccatacagGTCACGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAAATTTTTGACAGATGCCAAATTGGCTATAA
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--------------------------------------------------gttagtgatttcttctagacat-cctgttgtc---tcttagtgcatctatctgaatcatttatattctcgcagGTCATGGTGGTTCACGTGCTGCTGAGTATTTGAAGGAGCACTTGTTTGAGAACCTCATGAAACATCCGGAGTTCATGACAAATACAAAATTAGCATTAA
upper sequence: GLYMA14G31890.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtaagattttctactacatcacttgcatgggagaaatatagttctttaatttcagtgattgcaattgcattcatctgttatgcagttttggtaatatgccttaaattttaaattccatacagGTCACGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAAATTTTTGACAGATGCCAAATTGGCTATAA
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tagcaatatgcgttcatataatactcaga-aacagaatcatagattgttgact----tgatctctatt--tttcctcttcta---------------atatctgaagctttaa--tcatcacagGCCATGGTGGTTCACGTGCTGCTGAATACCTGAAGGAACACCTGTTTAACAATCTCATGAAGCATCCACAATTTTTGACAGACACCAAGCTGGCATTAA
upper sequence: GLYMA14G31890.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv16s0050g02570.t01 (Vitis vinifera), 3'ss of exon 3
gtaagattttctactacatcacttgcatgggagaaatatagttctttaatttcagtgattgcaattgcattcatctgttatgcagttttggtaatatgccttaaattttaaattccatacagGTCACGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAAATTTTTGACAGATGCCAAATTGGCTATAA
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-------------aaacactaaatccatgattttaagcttcttttttccttcctttccttatgaaaagaatgaaaaggattcaagtgtttacaat---tatgagatgt------cctaacagGTCATGGTGGTTCTCGTGCTGCGGAGTTTTTGAAGGAGCATCTCTTTGAGAATTTGATGAAGCATCCAGAGTTCATGACAAATACCAAATTGGCTATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattcatctgttatgcagttttggtaatatgccttaaattttaaattccatacagGTCACGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAAATTTTTGACAGATGCCAAATTGGCTATAA
taatatgccttaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattttctactacatcacttgcatgggagaaatatagttctttaatttcagtgattgcaattgcattcatctgttatgcagttttggtaatatgccttaaattttaaattccatacagGTCACGGTGGTTCTCGTGCTGCTGAGTATTTAAAGGAGCATCTTTTTGATAATCTCTTGAAGCATCCAAAATTTTTGACAGATGCCAAATTGGCTATAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG