Sequence
atgc intronic sequence ATGC exonic sequencegtgtaattgagtgtccctatccagataaagacatcaggagatttgatgcaaacatgcggctgtttcccccatttattgataatgatatatgccctttaaccattaaaaacaccattcttcagTCATGTTACTTGAGAAACACTGAGTGGGCATGTGGAGTGGCTGTGTATACAGGCAAGCCCAT
Basic information
species | Glycine max |
transcript | GLYMA12G33340.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------------------------------------------gtgtaattgagtgtccctatccagataaagacatcaggagatttgatgcaaacatgcggctgtttcccccatttattgataatgatatatgccctttaaccattaaaaacaccattcttcagTCATGTTACTTGAGAAACACTGAGTGGGCATGTGGAGTGGCTGTGTATACAGGCAAGCCCAT
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gtatcatgcatttttgaaaacatattttggtgcttcttttattttctttttcacccttgcatgccgtgactaaacagGGTGTTATTGAGTGCCCAAACCCGGATAAAGACATCCGAAGATTGGATGCAAACATACGGCTGTTTCCTCCATTTATTGATAACGACATTTGTCCATTGA-------------------------------------------------------------------------------------
upper sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G865163_T01 (Zea mays), 3'ss of exon 4
-------------------------gtgtaattgagtgtccctatccagataaagacatcaggaga--tttgatgcaaacatgcggctgtttcccccatttattgataatgatatatgccctttaaccattaaaaacaccattcttcagTCATGTTACTTGAGAAACACTGAGTGGGCATGTGGAGTGGCTGTGTATACAGGCAAGCCCAT--------------------------------
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gttaaacttttatttgttttatctgcttcacttttgttttaatttttcttttgcggcagcagggtaacccccattttactatg-gattttagtatgcattcatt--taacttcccattacctttatgaattaactaaac-agGGTGTGATCGAGT-GCCCAATACCAGATAAAGACATACGAAGATTTGATGCAAACATCCGCCTGTTTCCTCCATTCATTGATAATGACATTTGCCCATTGA
upper sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G411940_T01 (Zea mays), 3'ss of exon 7
gtgtaa--ttgagtgtccctatccagataaagacatcaggagatttgatgcaaacatgcggctgtttcccccattt----attgataatgatatatgccc-tttaaccattaaaaacacc-----attcttcagTCATGTTAC--TTGAGA----AACACTGAGTGGGCATGTGGAGTGGCTGTGTATACAGGCAAGCCCAT------------------------------------
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gttaaacttttatttgttttatctgcttcacttttgtttaatttttcttttgcggcagcagg-gtaacccccattttactatggattttagtatgcattcatttaacttcccattacctttatgaattaactaaacagGGTGTGATCGAGTGCCCAATACCAGATAAAGACATACGAAGATTTGATGCAAACATCCGCCTGTTTCCTCCATTCATTGATAATGACATTTGCCCATTGA
upper sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G44240.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgtaattgagtgtccctatccagataaagacatcaggagatttgatgcaaacatgcggctgtttcccccatttattgataatgatatatgccctttaaccattaa-aaacaccattcttcagTCATGTTACTTGAGAAACACTGAGTGGGCATGTGG--AGTGGCTGTGTATACAGGCAAGCCCAT-----------
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------gtaagacttcttgt--aaataatcatatcgttcctggctttccatactatttcctcttatcagattttatattaagctgtctatgttttcagGGTGTGATTGAATGTCCTGTTCCAGATAAGGATATTCGAAGATTTGATGCAAACATGCGCTTATTTCCGCCATTTATTGACAATGATGTCTGTTCTTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cccatttattgataatgatatatgccctttaaccattaaaaacaccattcttcagTCATGTTACTTGAGAAACACTGAGTGGGCATGTGGAGTGGCTGTGTATACAGGCAAGCCCAT
ctttaac putative branch site (score: 3)
ccattcttc putative PPT
ttattgataatgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtaattgagtgtccctatccagataaagacatcaggagatttgatgcaaacatgcggctgtttcccccatttattgataatgatatatgccctttaaccattaaaaacaccattcttcagTCATGTTACTTGAGAAACACTGAGTGGGCATGTGGAGTGGCTGTGTATACAGGCAAGCCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG