Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaatatttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g56646.1 (Oryza sativa), 3'ss of exon 4
gtatgtctgggggatgagatgctggagtgtttcacttgcttgctcagtgt--ttaatatttttgttgcccttcccagAATGCTACACAGAAA-AGTCAGAAGGTATTTGTCCATGTTCCTTCAG-AAATTGCTGCTCATGAAGTTGAGGAAATTG
| || | | || | |||| || || | ||||| | ||||| | || ||||||||||| || ||| ||||| ||||| ||||| ||||||||||||| |||| ||||| || || ||||||||||| |
----------------gtttattgtgcttgtccattgtcttgttctgtttcattaatgtacatgttgtcttttacagAATGCTACTCAAAAACAGTCAAAAGGTGTTTGTTCATGTTCCTTCAGCAAATAGCTGCCCACGAGGTTGAGGAAATCG
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G03160.1 (Glycine max), 3'ss of exon 4
-----------gtatgtc-tgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaa-----------tatttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
|||||| ||| || | | ||| | || | | | ||| || | ||| || | | | || ||||| || || |||||||| ||||||||| | ||||| || ||||| |||||| || ||||||||||||||||
gtaatcctgatgtatgtgatggtgggaggggagctagtgtttgctcaacacaaaattagtattccaagaaactgacatatagTTTATTCTGTGTACATAATGCCACTCAAAAAAGTCAAAAGGTATTTATACATGTGCCATCAGAGATTGCTACTAATGAAGTTGAGGAAATAT
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------gtatgtc-tgggggatgagatgctggagtgtttcacttgcttgctcagtgtt---------taatatttttgttgccctt--cccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
|||||| ||| || | ||| | || | || | ||| | |||||| | || || |||||||| || || |||||||| || || ||||| ||||| || ||||| |||||||||||||||||||||||||| |
gtacaaattaagtccgtcatatctttgatagaaatcttatatatctgttcttgctgatattttgcaaaagtaatcctgctgtatgtgatggtgggacgggagctagtgtttgctcaacactaaattagtactcaaagaaactaatatatagtttattctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------------gtatgtc-tgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaa-----------tatttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
| |||| | | || | | ||| | || | || | ||| || || ||| || | | | |||||||| || || |||||||| ||||| ||||| ||||| || ||||| ||||||||||||||||||||||||||
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA-
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------gtatgtctgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaatatttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
|| | | | | | || || | | || |||| | || || || |||||||||||| |||||||| ||||| || || || ||||| || ||||||||||||||||||||||||||||||| |
gtaagatacaaacccttccaaatattgtcccttttgtaaagttgtatgcttattataatcagatgctgattaa-acacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------gtatgtctgggggatgagatgc---tggagtgtttcacttgcttgct-cagtgttta-----atatttttg-ttgcc-----------------cttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
|| | | | || ||| || | || | || ||| || || | ||| |||| | | ||||| || ||||||||||| |||||||| || |||| ||||| || || ||| |||||||||| ||||||||||||||||||||||
gtaaataccagccaattttctaaccattttacttgctcgactgttaagttgcatctgacatacttgatttactttctgcattagttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------gtatgtctgggggatgagatgc---tggagtgtttcacttgcttgct-cagtgttta-----atatttttg-ttgcc-----------------cttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
|| | | | || ||| || | || | || ||| || || | ||| |||| | | ||||| || ||||||||||| |||||||| || |||| ||||| || || ||| |||||||||| ||||||||||||||||||||||
gtgaaagaggtaaataccagccaattttctaaccattttacttgctcgactgttaagttgcatctgacatacttgatttactttctgcattagttatatccatatatctaattgccttgatccgaacttctctctctgcagAATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTG
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------gtatgtctgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaatatttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
|| | | | | | || || | | || |||| | || || || |||||||||||| |||||||| ||||| || || || ||||| || ||||||||||||||||||||||||||||||| |
gttaaggaggtaagatacaaacccttccaaatattgtcccttttgtaaagttgtatgcttattataatcagatgctgattaa-acacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------------------------------------gtatgtctgggggatgagatg-ctggagtgtttcacttgcttgctcagt--gtttaat---atttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
| ||| | || || || ||||| | || || ||||| | || ||| | | ||||||||||| |||||||| |||||||| ||||||||||| || || |||||||||||||||||||||||||||||||
gtaagaactaagaacatctttaatgttttcttatttagctggtgcatgattgatcagttacattttattcagcttgaatcttgctgacttactgtctaagacatttcattaaaatgacttgttggtttactctaatgcttgcttatggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATTGCTGCTCATGAAGTTGAGGAAATTG
upper sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------------------------------gtatgtctgggggatgagatgctggagt-gtttcacttgc-ttgctcagtgtttaatatttttgttgccct----tcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
| | ||| | || | || | | |||| || || |||| || | | || | | | | |||||||| || |||||||| ||||| || |||||||| | ||||| |||||||||||||||||||||||||||||||
gtacaactaagaatatcataatgttttttcatttagctggtgcatgattgatcagttacatcataccaagcttgaatatggccagtttactgtttaagaagctccactgatattacttagtggtttactctaatgcttgcttatggttacagAATGCCACTCAGAAAAGCCAGAAAGTTTTTGTCCACATACCTTCTGAAATTGCTGCTCATGAAGTTGAGGAAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctggagtgtttcacttgcttgctcagtgtttaatatttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
gtttaat putative branch site (score: 4)
tttttgttgcccttcc CT-rich tract
tgtttaatatttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtctgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaatatttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT