Sequence
atgc intronic sequence ATGC exonic sequence...ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagAATTTGTCCTTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT
Basic information
species | Glycine max |
transcript | GLYMA14G01480.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagAATTTGTCC--TTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
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-------------------------------------ggattcattccttgtcaagtatcttgttagtaaagcac-atca-taaatttttgaatagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 11
ttgaaaatattatccaacctatattctaagaaactagttc--ttctttcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagA-ATTTGTCCTTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
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------------------------------------attcaatttcttgttaaagattctgtt-aataaagctcttcatacatcc---ttgagtataaatacataactattgtcaattatttcttacaattgctttccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAG
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatg-atcactgcaattttttataaacagAATTTGTCCTTAAATTTGATA--TGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
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----------------------------------------ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 10
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagAATTTGTCCTTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
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----------------------aacatgcacaattgacccctcatgcactagaattcaattc-------atcagtcatcacaagaacatct-atgtactctacaaat-----gatttgcta--caactggtttccagTGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAG
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagAATTTGTCCTTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
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-----------------------------------------------------------------gtaaa---gaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacc-tatgatcactgcaattttttataaacagAATTTGTCCTTAAATT--TGATATGC-AATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
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---------------------------------------gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 11
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagAATTTGTCCTTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
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--------------------------aaaggaaaaagaagtgcaaa---aagcatattcctggttatggacccattttctctttgtctttt--------gcattttggtttgaaccatcttctcttactgatgccagTGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAG
upper sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------------------------------ttgaaaatattatccaacctata---ttctaagaaactagttcttctttccta------attact-cagtttgatgtgaacctatgatcactgcaatttttt-------ataaa-cagAATTTGTCCTTAAATTTGATATGCAATCTAATTT----CAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
|| | | | | | | | | | | || ||| ||| || | | || || || || |||| | || | | ||| ||| ||| || | | || | || | | || | | || | |||||| ||||||||||| |||||||| || || || ||||| || ||||||||||| || |||||
gttatcttttatttattgtaccaccgaagtgggatattgttacgagt-tcactgggcttgtggagtgtcagtagtctggttgcatcttcttatgcagtaatgctgtagctttatttgaagtt-tgtgtgcagagattgtttcgaggatgtaagtcacagaatatcagtcaactcattctgttagcacatgttgcgcagTGGAGAGAGTATGGAGAATGCTTTGCGGGCGTGTTGCAAGGGCATCAAGATTGGAAAGATTCTAATACACCGGGAGGGAGATGACGGGAAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagAATTTGTCCTTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT
ttttttat CT-rich tract
aattttttataaaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacctatgatcactgcaattttttataaacagAATTTGTCCTTAAATTTGATATGCAATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - -ccaacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgca