Sequence
atgc intronic sequence ATGC exonic sequencegtaaggatgtcacttaagaatggcatgtcatttagttatttttatcaatctgtttatttgtcctacaattctacataaactgatcaaacactcggaatcagGGAAGCTTGTTTTTGCTGATCCTGTTCCCAAGGACAACGAAGCTGCTACTTGGAGAGAAAAATTAGATCAACTTTATAAAAGTTCATCACAGAGTTTTAG
Basic information
species | Glycine max |
transcript | GLYMA07G38890.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os07g33670.1 (Oryza sativa), 3'ss of exon 8
gtaaggatgtcacttaagaatggcatgtcatttagttatttttatcaatctgtttatttgtcctacaattctacataaactgatcaaacactcggaatcagGGAAGCTTGTTTTTGCTGATCCTGTTCCCAAGGACAACGAAGCTGCTACTTGGAGAGAAAAATTAGATCAACTTTATAAAAGTTCATCACAGAGTTTTAG---
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-------------------gtga-gtgtcttttggctcttactttccacatttttctta---ttgtgttgccaagtgaactg-ttggtttctc-----cagGCAAACTTGTCTTTGCTGAACCTGCCCCCAAGGAT---GAAGCTGCAACGTGGAAGGAGAAGATTGATCAGCTTTTTAAAAGTTCATCACAGAGTTTTAGGGT
upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G61850.2 (Arabidopsis thaliana), 3'ss of exon 8
gtaaggatgtcacttaagaatggcatgtcatttagttatttttatcaatctgtttatttgtcctacaattctaca-taaactgatcaaacactcggaatcagGGAAGCTTGTTTTTGCTGATCCTGTTCCCAAGGACAACGAAGCTGCTACTTGGAGAGAAAAATTAGATCAACTTTATAAAAGTTCATCACAGAGTTTTAG
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----------------------gtgtgtaa---aattccctttacagcttcgttgacttatt----ggttctggactttact--ttggatgtttttctatagGAAAGCTTGTTTTTGCTGAATCTGTCCCAAAGGACAATGAAGCTGCAAGCTGGCGGGAAAAGTTGGATCAGCTATATAAAAGTTCATCGCAAAGTTTTAG
upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ31555 (Selaginella moellendorffii), 3'ss of exon 8
gtaaggatgtcacttaagaatggcatgtcatttagttatttttatcaatctgtttatttgtcctacaa-ttctacataaactgat---caaacactcggaa---tcagGGAAGCTTGTTTTTGCTGATCCTGTTCCCAAGGACAACGAAGCTGCTACTTGGAGAGAAAAATTAGATCAACTTTATAAAAGTTCATCACAGAGTTTTAG
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-------------------------------------------------------gtgtgtacttcaaattctttgtaagctgcttttctgatcctcatacatttcagGAAAAGTAGTGTTTGCCGAGCCGATTCCAAAGGACAATGAAGCAGCCACTTGGAGAGAGAAACTAGATCAACTCTATAAAAGCTCGTCACAGAATTTTCG
upper sequence: GLYMA07G38890.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ38595 (Selaginella moellendorffii), 3'ss of exon 8
gtaaggatgtcacttaagaatggcatgtcatttagttatttttatcaatctgtttatttgtcctacaa-ttctacataaactgat---caaacactcggaa---tcagGGAAGCTTGTTTTTGCTGATCCTGTTCCCAAGGACAACGAAGCTGCTACTTGGAGAGAAAAATTAGATCAACTTTATAAAAGTTCATCACAGAGTTTTAG
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-------------------------------------------------------gtgtgtacttcaaattctttgtaagctgcttttctgatcctcgtacatttcagGAAAAGTAGTGTTTGCCGAGCCGATTCCAAAGGACAATGAAGCAGCCACTTGGAGAGAAAAACTAGATCAACTCTATAAAAGCTCTTCACAGAATTTTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatctgtttatttgtcctacaattctacataaactgatcaaacactcggaatcagGGAAGCTTGTTTTTGCTGATCCTGTTCCCAAGGACAACGAAGCTGCTACTTGGAGAGAAAAATTAGATCAACTTTATAAAAGTTCATCACAGAGTTTTAG
aactgat putative branch site (score: 3)
tttatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggatgtcacttaagaatggcatgtcatttagttatttttatcaatctgtttatttgtcctacaattctacataaactgatcaaacactcggaatcagGGAAGCTTGTTTTTGCTGATCCTGTTCCCAAGGACAACGAAGCTGCTACTTGGAGAGAAAAATTAGATCAACTTTATAAAAGTTCATCACAGAGTTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA