Sequence
atgc intronic sequence ATGC exonic sequencegtatgctttctatattcatttaggcattgtttcgcagtttgattagttttattctgccaaatcacattgaaggttgcataatctgaccatttctgtatttttctttcatatgaaatttgttattcatcattattttccctgtcttattatttttgaaggcttgcatatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
Basic information
species | Glycine max |
transcript | GLYMA05G30430.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 5
gtatgctttctatattcatttaggcattgtttcgcagtttgattagttttattctgccaaatcacattgaaggttgcataatctgaccatttctgtatttttctttcatatgaaatttgttattcatcattattttccctgtcttattatttttgaaggcttgcatatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
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--------------------------------------------------------------------------------gcacgatgccttgtgtgcaggccttggggccataagtcaataa-cataattttgcattgtgtactatcaact------------ataactagatgttattttctttat-------tgcagTTCGGGAAGAAAACTCACCCTGAATGTGCTCGATTTTCACCTGATGGCCAGTACCTTGTATCATGCTCAGTGGATGGAATCATTGAG
upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 5
gtatgctttctatattcatttaggcattgtttcgcagtttgattagttttattctgccaaatcacattgaaggttgcataatctgaccatttctgtatttttctttcatatgaaatttgttattcatcattattttccctgtcttat-tatttttgaaggcttgcatatctgacccttatgttttgtgtctgcttgtt-tagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
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---------------------------------------------------------------------------------------------------tgctgaagacagaatatttttaacatgctgtcaagtgagttttcttatctagcttttgatactaagttttataacatt---gcactgttcttgattcttgcagTTTGGGAAGAAAACTCATCCTGAATGTGCTCGATTTTCACCTGATGGTCAGTACCTTGTTTCATGCTCAGTTGATGGAATAATTGAA
upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgctttctatattcatttaggcattgtttcgcagtttgattagttttattctgccaaatcacattgaaggttgcataatctgaccatttctgtatttttctttcatatgaaatttgttattcatcattattttccctgtcttattattt-ttgaaggcttgcatatctgac---ccttatgttttgtgtc--tgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
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-----------------------------------------------------------------gttcata--ttcacactttaatagcttctttagcttagtggtctatga--tctgttgctcatgattattttgg--gttttctcatcagttgagttcttgtctaattttcatatctttttccttgtgctggtgctggtgcagTTTGGTAAAAAGAGTCATGCAGAATGCGCTAGATTCTCACCAGATGGACAGTTTCTTGCATCTTCTTCTGTGGATGGTTTTATCGAG
upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 6
gtatgctttctatattcatttaggcattgtttcgcagtttgattagttttattctgccaaatcacattgaaggttgcataatctgaccatttctgtatttttctttcatatgaaatttgttattcatcattattttccctgtcttattatttttgaaggcttgcatatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
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----------------------------------------------------------------------------------------------gagctattatttggttggtgtttagtttttcct--ttatgctattgggttcttcagttgttttgcttttcatctc-atgtgttgtgctg-gtgttacactg--cagTTTGGAACAAAAAGTCATGCAGAATATGCTCGGTTTTCTCCAGATGGGCAGTTTCTTGTGTCTTGCTCCGTGGATGGATTTATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatttttgaaggcttgcatatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
atctgac putative branch site (score: 3)
tctgctt putative PPT
ttatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctttctatattcatttaggcattgtttcgcagtttgattagttttattctgccaaatcacattgaaggttgcataatctgaccatttctgtatttttctttcatatgaaatttgttattcatcattattttccctgtcttattatttttgaaggcttgcatatctgacccttatgttttgtgtctgcttgtttagTTTGGGACAAAAAGTCATGCAGAATGTGCTTGCTTTTCACCAGATGGGCAGTTTCTTGTATCATGCTCAGTTGATGGGTTTATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG