Sequence
atgc intronic sequence ATGC exonic sequence...ttgtatcacatttttaactttttcttcctaccagtgaggcccttttacatgttatttatgctagtggatatttaaatggttgcttcactatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
Basic information
species | Glycine max |
transcript | GLYMA19G44820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g48790.1 (Oryza sativa), 3'ss of exon 4
ttgtatcacatttttaactttttcttcctaccagtgaggcccttttacatgttatttatgctagtggatatttaaatggttgcttcac-tatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
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---------------------------gtattagaaacaactctggattctttcgttagaaaagcatacacatacactaacctgcaatgtttgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
upper sequence: GLYMA19G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G044495_T01 (Zea mays), 3'ss of exon 4
ttgtatcacatttttaactttttcttcctaccagtgaggcccttttacatgttatttatgctagtggatatttaaatggttgcttcactatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
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----gttactgacaagcatatttgtttctctcagcgtaccttttttctctctcttcaaaatccgtag----tctaaccacggagcattcatccctttcagATGGCGGACCCCTTGACTGCTTTGATACATGCCGTTCAAGTGATGAATTTCCTCAAGACATTGATCTTGAGAACTGTAAAAGAAAGGGAGGAGGCTGCTA
upper sequence: GLYMA19G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G46710.1 (Arabidopsis thaliana), 3'ss of exon 4
ttgtatcacatttttaactttttcttcctaccagtgaggcccttttacatgttatttatgctagtggatatttaaatggttgcttcactatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
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----gtca-gtaataaaattgaattttcttttaatgaaacagttg-attctttagttata-tagttttgaatctcatgaaaatgttttgatgttgt--agATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG
upper sequence: GLYMA19G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0048g02830.t01 (Vitis vinifera), 3'ss of exon 5
-ttgtatcacatttttaactttttcttcctaccagtgaggcccttttacatgttatttatgctagtggatatttaaatggttgctt-cactatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
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attggcatgtgtagttaaaatggctattgtgaaatttt--ccttctttcaagacaatttggctacagtgtaagtaaatgattgtttattttgtttgatacagATGGCCGATCCTTTGACTGCCTTGATTCATGCGGTGCAAGTTATGAACTTCCTTAAGACACTGATTATGAAGACCCTTCAAGAAAGAGAAGAATCAGCTG
upper sequence: GLYMA19G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------ttgtat-cacatttttaactttttcttcctaccagtgaggcccttttacatgttattt----atgctagtggatatttaaa---tggttgcttcactatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
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gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactctt-cacctcattttggaacgctaactgaagcctaacacctgtttcgacctctata-tctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatgttatttatgctagtggatatttaaatggttgcttcactatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
atatttaaatggtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtatcacatttttaactttttcttcctaccagtgaggcccttttacatgttatttatgctagtggatatttaaatggttgcttcactatgctatgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTCATGAACTTCCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATGAATCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - cctacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - tttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttcac