Sequence
atgc intronic sequence ATGC exonic sequencegtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacatattaattttactatagcccgggcagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
Basic information
species | Glycine max |
transcript | GLYMA02G44720.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G44720.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g59360.1 (Oryza sativa), 3'ss of exon 3
gtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacatattaattttactatagcccgggcagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
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--------------------------------------gtacgtgcctcttctggttctccattttgcatcgtttcatttgggatgtttgaaattttaactaacaatgcaatttttggttgtt-----aattagATCACCCGTGGATCAAGGAAGATGGAGAAGCACCTGACACGCCGCTTGACAACGCTGTCATGAACAGGCTCAAGCAGTTCAGGGCTATGAACCAATTCAA
upper sequence: GLYMA02G44720.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G472311_T01 (Zea mays), 3'ss of exon 1
gtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacatattaattttactatagcccgggcagattggttca-atgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
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----------------------------gtaagtagccagat-cggttacttcatatat--atactactactcatcatatggatcgatggacatgtggcctcaacacgcaagAACTTGT--------------AGATCACCCATGGATCAAAGAAGACGGAGACGCACCAGACACGCCACTTGACAACGTTGTTCTCGACAGGCTCAAGCAGTTCAGGGCCATGAA---------
upper sequence: GLYMA02G44720.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G12180.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacatattaattttactatagcccgggcagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
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-----------------------------------------------gtaagcatctacaaaatatataaaaactgtaaaagcataa--caatatattatctctaatgt-tatcttcctttgt-------aaagACCATCCATGGATCAAGGAGGATGGAGAGGCACCAGATGTTCCTCTTGATAATGCGGTGATGTCCAGGCTCAAACAATTCAAAGCAATGAACAATTTCAA
upper sequence: GLYMA02G44720.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G19360.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacatattaattttactatagcccgggcagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
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---------------------------------------------------gtaagcagctcttatcttaaaagctcc-tatatatatttcattgaactcttcttg---acatttttgttgttttaaa-----gATCATCCATGGATCAAGGAGGATGGAGAAGCACCGGATGTTCCTCTTGACAATGCAGTGATGTCTAGGCTCAAGCAGTTCAAAGCAATGAACAACTTTAA
upper sequence: GLYMA02G44720.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g03150.t01 (Vitis vinifera), 3'ss of exon 3
gtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacata-ttaattttactat-agcccgggcagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
||| ||| | ||| | | || || |||| |||||| | | | |||| ||| ||| |||| ||||| || ||| | | ||||||||||||||| |||||||||||||||||||| ||||| ||||||||||| ||||| | | ||| |||||||||| |||||||||||| | |||||
---------------actgagtttggagatatttaggaaaactttgtttgaagtcatacttaattatgatgttagccattgcacattt-----------ttctgataaaattcaattttttct----------tagATCATCCATGGATTAAGGAGGATGGAGAAGCACCTGATACTCCTCTTGACAATGCAGTTTTTGAAAGGTTCAAACAGTTTAGAGCAATGAACAAGTTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
ttctaat putative branch site (score: 2)
acattttactttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtataatattgacttcctttctatgaattcgactacatgttcttgatttacatattaattttactatagcccgggcagattggttcaatgcaattctaataaagcacattttactttatgtgaaaaacagATCATCCATGGATCAAGGAGGATGGAGAAGCACCAGATACACCTCTTGACAACGCAGTACTGAATAGGCTCAAACAGTTCAGAGCAATGAACGAATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA