Sequence
atgc intronic sequence ATGC exonic sequencegtaagcctgtgcttcaattaatatgttgtttttcagttgtttggtcccagttatgactcaccatgtccttaccctcaagactagttgaacagctatgctattttaatgacatggttgaacttttaaccctttatacttgtcttggatagtttaaaacttaattgactggaaattgttgttgtgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTCCGAGCACGTTTCTATATGGAGCCAGATATGCAAGACAATGGCTCTGCAGGTGATGGCAATGGTTA
Basic information
species | Glycine max |
transcript | GLYMA20G28970.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G43810.2 (Arabidopsis thaliana), 3'ss of exon 20
gtaagcctgtgcttcaattaatatgttgtttttcagttgtttggtcccagttatgactcaccatgtccttaccctcaagactagttgaacagctatgctattttaatgacatggttgaacttttaaccctttatacttgtcttggatagtttaaaacttaattgactggaaattgttgttgtgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTCCGAGCACGTTTCTATATGGAGCCAGATAT---GCAAGACAATGGCTCTGCAGGTGATGGCAATGGTTA
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------------------------------------------------------------------------------------gtaaataacaacatttcttcttcttcttcgt-gtacccgcaaatatg---acgaaaatcagcaaactcatatgttcttttatttt---ctgatgttgtacagTTCCTCCAGCGTATTATGCTCATCTTGCAGCATTTCGAGCACGTTTCTACCTGGAACCGGAGATAATGCAAGACAACGGATCACCGGGTAAAAAGAACAC---
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 18
gtaagcctgtgcttcaattaatatgttgtttttcagttgtttggtcccagttatgactcaccatgtccttaccctcaagactagttgaacagctatgctattttaatgacatggttgaacttttaaccctttatacttgtcttggatagtttaaaacttaattgactggaa--attgttgttgtgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTCCGAGCACGTTTCTATATGGAGCCAGATATGCAAGACAATGGCTCTGCAGGTGATGGCAATGGTTA
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----------------------------------------------------------------------------------------tcctttgaagttctttgttcaaattgtcctccttgaggagctccatcattttgttctatgagctgcaactgaaatagctaaatccatggctcatttgcagTTCCTCCAGCATATTATGCACATTTAGCAGCATTTCGAGCCCGATTCTACATGGAGCCTGACATGCAGGAGAATGGTTCAAATGGAGGTGGCAGTG----
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 18
gtaagcctgtgcttcaattaatatgttgtttttcagttgtttggtcccagttatgactcaccatgtccttaccctcaagactagttgaacagctatgctattttaatgacatggttgaacttttaaccctttatacttgtcttggatagtttaaaacttaattgactggaaattgttgttgtgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTCCGAGCACGTTTCTATATGGAGCCAGATATGCAAGACAATGGCTCTGCAGGTGATGGCAATGGTTA
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-------------------------------------------------------------------------ccggagaatgttcaaaattcta-gatgcttt---gtcatttttaa---tttaag--tgtgagttcacattacttactagaatacgacgttctctaa----tgatgaatcgcagTTCCTCCGGCTTATTATGCGCATTTGGCTGCTTTCCGAGCGCGCTTCTACATGGATCCAGAAGCTTCCGATACTGGATCTCTAACTAGTGGGATGGGAGG
upper sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 19
gtaagcctg----tgcttcaattaatatgttgtttttcagttgtttggtccca-gttatgactcaccatgtccttaccctcaagactagttgaacagctatgctattttaatgacatggttgaacttttaaccctttatacttgtcttggatagtttaaaacttaattg----actggaaattgttgttgtgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTCCGAGCACGTTTCTATATGGAGCCAGATATGCAAGACAATGGCTCTGCAGGTGATGGCAATGGTTA
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gtatgttcaaaaatcttctacgtcatataatggtttttgtctattcaacaaaatgtctcggctaagcgcattatt----tgaaatcttattcaacgttcttggtagacctgggat-tgggtgta-tccgaatatcttgattttggttgatatcgcttagaatcaaaatgtaacgttttgtattgatgatttgcagTTCCTCCAGCATATTATGCACATCTAGCTGCTTTTCGTGCCAGGTTCTACATGGATCCAGAAGCTTCAGATACTGGTTCTGTTACTAGTGGGTTGGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatacttgtcttggatagtttaaaacttaattgactggaaattgttgttgtgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTCCGAGCACGTTTCTATATGGAGCCAGATATGCAAGACAATGGCTCTGCAGGTGATGGCAATGGTTA
aattgac putative branch site (score: 3)
atagtttaaaacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcctgtgcttcaattaatatgttgtttttcagttgtttggtcccagttatgactcaccatgtccttaccctcaagactagttgaacagctatgctattttaatgacatggttgaacttttaaccctttatacttgtcttggatagtttaaaacttaattgactggaaattgttgttgtgcagTTCCTCCAGCATATTATGCACATTTAGCAGCGTTCCGAGCACGTTTCTATATGGAGCCAGATATGCAAGACAATGGCTCTGCAGGTGATGGCAATGGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG