Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 22
gtttg-tttttcatatcctcccagtttacttattcacat-gagtgaaggtagccaag---atgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCT--TACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT------------------
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gtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTA--GTGAGCGAGGGTAGCCAAGAT---GTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 22
--------gtttgt-ttttcatatcctcc-cagtttacttattcacatgagtgaaggta-gccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT------------------
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gtatgattctttatattatcttgtattccacagccagcttaagggcatgtgcacatgcacacaaacatatgcttttttgtttcgttgctgatc---tcatcttttatattt-cttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTA--GTGAGCGAGGGTAGCCAAGAT---GTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 22
gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATAT-TGTGAAAAGCGGGATCC-TACACTTGCTGTTGTT
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------------------------gtgcgtctctctatctttcatctccactatcattgccatgttcat----ttctcatttaattttttatgcatagGAATCGTCTCCGCTTGC-TCACTCAATTCTTGGAGCATCTTGTAAGTGAAG-GAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
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----gtgtgcaagttttttccaccctgcatccccaaattaccata-----ttattttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGG-AGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGT----GCATAATGCTCTGGGTAAAATTATCATTGAC-----------
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 20
gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggta-----aaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
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--------------gtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcattgcactttctatgcgcagAAATCGTCTTCGCTTGCTTACTCAGTTTTTGG-AGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGT----ACATAATGCTCTGGGTAAAATTATCATTGAC-----------
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 22
gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
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--gtgtgctagttttctctctattttgc--atctccagtatcgttgctatgttcatttctcatgttctttttttatgcatagGAATCGTCTCCGATTGCTTACTCAATTCTTGG-AGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGT-------ACATAATGCCCTGGGTAAAATCAT-TATTGAC-------
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtag--ccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCT--GAGCATTTCCTTACTACC--AACCCAT----TTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
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gtgaatccttttggtcatcctggtttgcgttcataattatgtctgtttagttctggaaactctaatatgtttctgctttttcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAA-ATTATCATAGAC-----------------------
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
----gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCT--GAGCATTTCCTTACTACC--AACCCAT----TTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
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gtgcgaacccttttagcatcttga-atttcgttcatatgtatgctattttgttctttaggctctaatatgtata-tgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAA-ATTATCATAGAC-----------------------
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
----gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
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gtgcattgtttttacctgtgtaccgtttccattaatatttttaattcttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGG-AGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCAT----AATGCTCTGGGTAAAATCATCATAGAC-----------
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 22
---gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggta-aaatcatcattgacagCAACAACAATCCT--GAGCATTTCCTTACTACC--AACCCAT----TTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
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gtgatgtgtccctaccatatgccctgttcgg--gttcactttctt---tttacttcaattgcttatgctttgcatgtggttttcagAAATCGACTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCTCTGGGTAAA-ATCATTATAGAC-----------------------
upper sequence: GRMZM2G111355_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 22
--------------------gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCT--GAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
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atattagaactaggttgcgtttttaaatgtctaaacattttagtgtcacgatttaaacatcctgacgtcgtcgagaactgatgagttgtggggtttatag- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
taaaatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttttcatatcctcccagtttacttattcacatgagtgaaggtagccaagatgtgcatgtccataatgctcttggtaaaatcatcattgacagCAACAACAATCCTGAGCATTTCCTTACTACCAACCCATTTTACGACTCTCGTGTTGTGGGTAAATATTGTGAAAAGCGGGATCCTACACTTGCTGTTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT