Sequence
atgc intronic sequence ATGC exonic sequence...ttagttctagtttcgattcccagatcaattatccctatattgccagttgcatcatgtggtgttgggatactaatattaggacatcatgtttgaaatgcagATGTGGATTGCAAAGGCTGAGTACGATGAGGCTGGTCCTTCAATTGTACACAGGAAATGCTTCTAAATGCTGCACAGCCTACAGGGTAGCTTGGTGAAAG
Basic information
species | Glycine max |
transcript | GLYMA11G14880.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04570.t01 (Vitis vinifera), 3'ss of exon 4
ttagttctagtttc-gattcccagatcaattatccctatattgccagttgcatc----atgtggtgttgggatactaatattaggacatcatgtttgaaatgcagATGTGGATTGCAAAGGCTGAGTACGATGAGGCTGGTCCTTCAATTGTACACAGGAAATGCTTCTAAATGCTGCACAGCCTACAGGGTAGCTTGGTGAAAG-----
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----ctatattctctgtttttcagacattttttttcctcactccaagatttgttcttgatgtagcaatttgctacaagtact-gaatgtgatatttgtaatgcagATGTGGATAGCAAAGGCAGAGTATGATGAATCTGGGCCATCTATTGTGCATAGGAAATGCTTCTAAAT--TGGCCAG---ATGGGGGAGGTAGAAGAAAGCCAGT
upper sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 5
-------------------------ttagttctagtttcgattcccagatcaat-tatccctatattgccagttgcat-catgtggtgttgggatactaatattaggacatcatgt---------ttgaaatgcagATGTGGATTGCAAAGGCTGAGTACGATGAGGCTGGTCCTTCAATTGTACACAGGAAATGCTTCTAAATGCTGCACAGCCTACAGGGTAGCTTGGTGAAAG-
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gtaatgtatttgactcgtgtctgagttgcatttcgtgtttttttttatgtcttcatgtctttgtttcttcaaatgctcgcgtttgtcgaggctgtaatctttctggaatttaatccgtttacttgttgtggtgcagATGTGGATTGCGAAGTCGGAGTACGATGAGTCAGGTCCATCAATTGTGCACAGGAAGTGTTTCTAGA-GCAGTGCGACACATCTTTTGCTTTTTTCAGCAC
upper sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 3
ttagttctagtttcgattcccagatcaattatccctatattgccagttgcatcatgtggtgttgggatactaatattaggacatcatgtttgaaatgcagATGTGGATTGCAAAGGCTGAGTACGATGAGGCTGGTCCTTCAATTGTACACAGGAAATGCTTCTAAATGCTGCACAGCCTACAGGGTAGCTTGGTGAAAG
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----------------------------gtaccacaacatt--cttttgc-tcgt-ttttcttatcagccttgtttttctttttctttttt----cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG----------------------------------
upper sequence: GLYMA11G14880.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 3
ttagttctagtttcgattcccagatcaattatccctatattgccagttgcatcatgtggtgttgggatactaatattaggacatcatgtttgaaatgcagATGTGGATTGCAAAGGCTGAGTACGATGAGGCTGGTCCTTCAATTGTACACAGGAAATGCTTCTAAATGCTGCACAGCCTACAGGGTAGCTTGGTGAAAG
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----------------------------gtaccacaacatt--cttttgc-tcgt-ttttcttatcagccttgtttttctttttcgtttct----cgcagATGTGGATTGCAAAGTCCGAGTACGATGAGTCGGGTCCATCGATTGTGCACAGAAAGTGCTTCTAG---------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgcatcatgtggtgttgggatactaatattaggacatcatgtttgaaatgcagATGTGGATTGCAAAGGCTGAGTACGATGAGGCTGGTCCTTCAATTGTACACAGGAAATGCTTCTAAATGCTGCACAGCCTACAGGGTAGCTTGGTGAAAG
tactaat putative branch site (score: 1)
atactaatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagttctagtttcgattcccagatcaattatccctatattgccagttgcatcatgtggtgttgggatactaatattaggacatcatgtttgaaatgcagATGTGGATTGCAAAGGCTGAGTACGATGAGGCTGGTCCTTCAATTGTACACAGGAAATGCTTCTAAATGCTGCACAGCCTACAGGGTAGCTTGGTGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - ttcccag
- - - - - - - - - - - - - - - - - - - - - -cagttgc
- - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt