Sequence
atgc intronic sequence ATGC exonic sequencegtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g03250.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G008234_T01 (Zea mays), 3'ss of exon 2
---gtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG
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tgcgtgcctgatactgttgctgagggagctgagctgagcttattgtactatataataa--tggttataaaaaaaacatgtctgcatgtgt--gcctgcgtgcagCTGGAGGACTACCAGGATGAGCTGGAGGAGATGAAGAACATGACGCGGCAGGAGTACGTGGCGCACCTCAGGAG
upper sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S131_131V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------gtaattaatc--aattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgt---atgtatgtatg-cagCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG
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gtatgtcatagaacgtgtgccctcatgtcattttgctgcaagtaaatgtgtccacaactgttctgagcttgatgacaaggaatg-tggtgggtgtgatgcttagtagttctgaggaatggtgcctcatgtacgtggaatggtggaatgt-tgtgcggcagCTTGATACATACGAACAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTTGCCTCGTTGAGAAG
upper sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S66_255V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------gtaat-taatcaattcaa--ttaaaatttttgattctgtaagtactgttaatta---attagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagCTG--GAGGAC-TACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG
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gtacgtgatgagtggtgtggtgagatggggtttgaggcggttgacagttgaggggcggagtggcagggatgggttgggtgcggtgctgatgaccgtggaatggtggatgggtgtgcaacagTTGAGTACGTATGAGGCGGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCGTCGTTGAGAAG
upper sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S131_139V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------gtaattaatc--aattcaat--taaaatttttgattctgtaagtactgttaattaattagtt--ggttaattgaataatgtgcatgcatatgtatgta----tgtatg-cagCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG
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gtaagtcatgaatcgtgtgccgtcatgtcattctgccgctaattaatgtgtccacaagtattctgagcttgacgccaaggcatgtggcgagcgtgatgctctgagcttagcagttctgaggaacggtgcctcatgcacgtggaatggtggaatgttgtgcgacagCTTGGTACATATGAAAAAGAGCTGGAGGAGATGAAGAACATGTCTCGGCAGGAGTATGTGGCCTCGTTGAGGAG
upper sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ21317 (Selaginella moellendorffii), 3'ss of exon 4
gtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG
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-----------------gtgagattccttcctct---tgtattattcatgaactcacaagaccgt-gtgtaaactacgt---tttgattg---gcat-cagCTAAGTGACTATGAAAAGGAGCTAGAGGAGATGAAACACATGACACGGCAGGAGTTTGTGGCTTCCCTTAGAAG
upper sequence: LOC_Os07g03250.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ26861 (Selaginella moellendorffii), 3'ss of exon 4
gtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgc-atatgtatgtatgtatgcagCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG
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-----------------gtaagattccttcctct---tgtattattcatgaactc--------acaagaccgtgtgtaaactacgttttggttggcat-cagCTAAGTGACTATGAAAAGGAGCTGGAGGAGATGAAACACATGACACGGCAGGAGTTTGTGGCTTCCCTTAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG
ttaattgaataatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattaatcaattcaattaaaatttttgattctgtaagtactgttaattaattagttggttaattgaataatgtgcatgcatatgtatgtatgtatgcagCTGGAGGACTACCAGGAGGAGCTGGAGGAGATGAAGAACATGACAAGGCAGGAGTATGTGGCTCACTTAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG