Sequence
atgc intronic sequence ATGC exonic sequencegtaatttgttctttctcaaggatctatgttacttttcaagttctatagatgataatcatctcatgatttctttccgctaattttctgcagATATGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTGTATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
Basic information
species | Glycine max |
transcript | GLYMA12G04780.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G04780.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 4
gta-atttgttctttctcaaggatctatgttacttttcaagttc-tatagatgataatcatctcatgatttctttccgct--aattttctgcagATATGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTGTATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
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gtatatatatagataccctct--cttctttcagttatcaggctcatattgtttctttacattttatcttcttacacctttttaactttctgcagATATGTTTCACCGGAATATGCAAGTACTGGTATGCTCAATGAGTGTAGTGATGTCTACAGTTTCGGTGTTCTGCTCATGGAGATCATTACAGGAAGGAGC
upper sequence: GLYMA12G04780.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0063g02510.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtaatttgttctttctcaaggatctat--gttacttttcaagttctatagatgataatcatct---catg---------atttctttccgctaattttctgcagATATGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTGTATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
| | | | ||| |||| || | | |||| ||| || || || || || | | |||| || || | | ||||||| |||||||| | || |||||||||||| |||||||||||| ||| | |||||||| ||||| ||||||||||| || ||||||||||| || ||||| |||
gtatgttcttcctcggtttcctataatatttttcaataatttgttagttagatttaaacttgaatgtattatttctctgtacacatgtattattaagttatttatcatcatttttctgtagATATGTCTCTCCCGAGTATGCAAGCACGGGTATGCTTAGTGAAGGGAGTGATGTCTATAGTTTTGGAGTTCTACTTATGGAGATAATTACTGGAAGGAGC
upper sequence: GLYMA12G04780.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------gtaatttgttctttctc---aaggatctatgttact--------tttcaagt-----tctatagatgataatcatctcatgatttctttccgctaatt--ttctgcagATATGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTGTATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
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gtaagcgtaaagtatgatttattgcctcgttgtaacaataattgcagctagcaacggtgacaagtatttgtttgtctttcatggttttctccttgagtcgttacgatggttgtttttgcagGTATGTAGCCCCCGAGTACGCGAACACGGGCCTGCTGAACGAGCGAAGTGATGTGTACAGCTTTGGGGTGCTTCTCATGGAGATTATCACCGGGCGAGAT
upper sequence: GLYMA12G04780.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------------gtaatttgttctt-tctcaaggatctatgttacttttcaagttctatagatgataatcatctcatgatttctttccgctaattttctgcagATATGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTGTATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
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gtaagctcaaggccctcctctggattgtattgtattgttgaaacagtagttgcagttataaacggcatttaatgtcgatttcttctagtcacatagttttatgtcgcgtgt----ttctcaacgttctagtc--cccatccccattctttggctgtatcactcagGTACGTAGCGCCGGAGTACGCGAACACGGGCCTGCTGAATGAGCGAAGCGATGTGTACAGCTTTGGGGTGCTTCTCATGGAGATCATCACGGGGCGAGAT
upper sequence: GLYMA12G04780.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36811 (Selaginella moellendorffii), 3'ss of exon 5
gtaatttgttctttctcaaggatctatgttacttttcaagttctatagatgataatcatctcatgatttctttccgctaattttctgcagATATGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTGTATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
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-------------------------gtatgagaattcaatcctctttgctcgcgaacgatcaaagtttttgttc------tttgtcgcagCTATGTCGCTCCAGAGTACGCTAACACTGGTCTACTCAACGAGAGAAGCGACGTTTATAGCTTTGGAGTTCTTCTCATGGAGATGATCACTGGGAGAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaagttctatagatgataatcatctcatgatttctttccgctaattttctgcagATATGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTGTATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
cgctaat putative branch site (score: 3)
ttttctgc CT-rich tract
taattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttgttctttctcaaggatctatgttacttttcaagttctatagatgataatcatctcatgatttctttccgctaattttctgcagATATGTTGCACCTGAGTATGCAAGCTCGGGTATGCTTAATGAGCGCAGTGATGTGTATAGCTTTGGAGTTCTTCTCATGGAGATAATCACAGGAAGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC