Sequence
atgc intronic sequence ATGC exonic sequence...ctatttggaagtttcatcctggattttggccattatccatcagttcttggtaacacgatgtctgctacactgttaacatagattgctttcttcctgtcagGTTGAGCACATGTTAAATGACAGATTGCTTCAGTTTGTCAATATTGATTTACAAGAGGTCAAG
Basic information
species | Glycine max |
transcript | GLYMA18G51810.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 4
ctatttggaagtttcatcctggattttggccattatccatcagttcttggtaacacgatgtctgctacactgttaacatagat-----tgctttcttcctgtcagGTTGAGCACATGTTAAATGACAGATTGCTTCAGTTTGTCAATATTGATTTACAAGAGGTCAAG
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-----ttgtgatcccaaccttcacttcagccatttcattctaggaacacgcggcctatgttttcttaccttgctgtcatctgtgttaatgtctatttgctggcagGTTGAGCACATGCTAAATGACAGATTGCTGAATTTTGTGGACATTGATTTGCATGATGTTAAG
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 1
ctatttggaagtttcatcctggattttggccattatccatcagttcttggta-acacgatgtctgctacactgttaacatagattgct--ttc---ttcctgtcagGTTGAGCACATGTTAAATGACAGATTGCTTCAGTTTGTCAATATTGATTTACAAGAGGTCAAG
| | | | ||| | || | | | | | |||| | || | | | | | || | | || || ||| |||||| ||||||||||||||||||||||||||||| || | ||||| | |||||||| || || || |||
-----tactatctccgccctag-ttctaacaaatttatatcatgccatgacacatctaacttttagtaatttacctgctctaatctctgattcggtttcctgacagGTTGAGCACATGTTAAATGACAGATTACTGAATTTTGTTGACATTGATTTGCATGATGTGAAG
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 4
---ctatttggaagtttcatcctggattttggccattatccatcagttcttggtaacacgatgtctgctacactgttaacatagattgctttcttcctgtcagGTTGAGCACATGTTAAATGACAGATTGCTTCAGTTTGTCAATATTGATTTACAAGAGGTCAAG
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ttatcttttccacttctgaaaatgatttttttgcatgcttaat---ttgatgttaagaggttgttccttgtctaatattttttaattgttccttttttttcagGTTGAGCACATGCTAAATGACCGGTTGATACAATTTGTGAATATTGATTTGCATGATGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttggtaacacgatgtctgctacactgttaacatagattgctttcttcctgtcagGTTGAGCACATGTTAAATGACAGATTGCTTCAGTTTGTCAATATTGATTTACAAGAGGTCAAG
tgttaac putative branch site (score: 2)
ttgctttcttcctgtc putative PPT
ttaacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctatttggaagtttcatcctggattttggccattatccatcagttcttggtaacacgatgtctgctacactgttaacatagattgctttcttcctgtcagGTTGAGCACATGTTAAATGACAGATTGCTTCAGTTTGTCAATATTGATTTACAAGAGGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - tcctgga
- - - - - - - - - - - - - -ggccatt
- - - - - - - - - - - - - - - - - -tccatca
- - - - - - - - - - - - - - - - - - - - - gttcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctac