Sequence
atgc intronic sequence ATGC exonic sequencegttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctctattttattgcagAGATGGCAAAGTCTAAGAATCACACAGCGCACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
Basic information
species | Glycine max |
transcript | GLYMA15G15320.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G15320.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G068496_T02 (Zea mays), 3'ss of exon 1
gttcgtatcttcaatttctgtaacaaat--tcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctctattttattgcagA-----GATGGCAAAGTCTAAGAATCACACAGCGCACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
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----gtactcctcgtcttcctcccgagtcctcctccggattcgatgttcgtctcctgatttattggtggaaccgcagGTGACTAGGAGCAGTAGCGAGAGGGATTCTGGATGGCCAAGTCGAAGAACCACACGGCGCATAACCAGTCGTTCAAGGCGCACAAGAACGGCATCAAGAA------------------------------
upper sequence: GLYMA15G15320.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S58_102V6.2 (Physcomitrella patens), 3'ss of exon 1
----------gttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctctattttattgcagAGATGGCAAAGTCTAAGAATCACACAGCGCACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
| | | | | | || || | ||||| | || || | | | | | ||| | ||| || |||| || | | ||||||| ||||| ||||||||||| || ||||| |||||||||||| |||||| || || |||||||| |||| || | | ||
ttagttcggagatgatttagttgaattttggag--gattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagCA--GGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTC------
upper sequence: GLYMA15G15320.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S58_102V6.1 (Physcomitrella patens), 3'ss of exon 1
-------gttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctctattttattgcagAGATGGCAAAGTCTAAGAATCACACAGCGCACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
| | | | | | || || | ||||| | || || | | | | | ||| | ||| || |||| || | | ||||||| ||||| ||||||||||| || ||||| |||||||||||| |||||| || || |||||||| |||| || | | || |
gttcggagatgatttagttgaattttggag--gattctgggtagttagcattggagcttctccatgtttcctgcattgagtttttcattcgctcgatagca--gGTAAGATGGCCAAGTCCAAGAATCACACCGCACACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAACACAAATATGCCTCAAG---
upper sequence: GLYMA15G15320.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_253V6.2 (Physcomitrella patens), 3'ss of exon 1
gttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctcta-ttttattgcag-
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agcaatagtttctagtgtggcagctgtggccccagggactg-gtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagcagGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTCAAG---
upper sequence: GLYMA15G15320.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
---gttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctcta-ttttattgcag-
|| ||| | | | | | | | || | ||||| | | | | || | | | ||||| || | |||| | |||| ||||||| ||||| ||||| ||||| |||||||| |||||||||||| |||||| || || |||||||| |||| |||| ||| ||
tgcagcaatagtttctagtgtggcagctgtggccccagggactg-gtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttctattctttcccttctcatcgtcctttcattttgctctattttattgcagAGATGGCAAAGTCTAAGAATCACACAGCGCACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
ttctttcccttctcat CT-rich tract
tctattttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctctattttattgcagAGATGGCAAAGTCTAAGAATCACACAGCGCACAATCAGTCCTACAAGGCCCACAAAAACGGCATCAAGAAACCCAAGAGGCATCGCCACACTTCCACCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG