Sequence
atgc intronic sequence ATGC exonic sequencegtaggtatgcatatattttgctttggtgtgttgtagcattataagaatcacttcatgctatcacagttgcactcttggagattcaaaactattctccattcatgctatgttgatatgtctggtatgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G372709_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g40470.1 (Oryza sativa), 3'ss of exon 9
gtaggtatgcatatattttgctttggtgtgttgtagcattataagaatcacttcatgctatcacagttgcactcttggagattcaaaactattctccattcatgctatgttgatatgtctggtatgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
| | || | | |||| || |||| | | || | |||| ||| ||||| || || || | || || ||| || || || |||||||||||| ||||||||| || ||||| ||||| || ||||| ||||| |||||| |||||||||| || |||||||| || ||||| |||||| |
------------------atccctagtccaatatgaggggataacaa--actt---gtgagcattatgccactattgcggattc----tcatgctgggatctt----tgactccatatcttgtttgcgc-----agTTCCACTATGCTGTTTTCTTTGCTTACATAAGGCTACGGGAGCAGGAGATTAGGAACTTGATGTGGATATCAGAGTGTGTTGCGCAGAATCAGAAGAACA--------------------------------
upper sequence: GRMZM2G372709_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G49110.1 (Glycine max), 3'ss of exon 10
gtaggtatgcatatattttgctttggtgtgttgtagcattataagaatcacttcatgctatcacagttgcactcttggagattcaaaactattctccattcatgctatgttgata-tgtctggtatgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
|| | | | || | | ||| | || | | || | | | || || || | | | | ||| | ||| |||| || |||| ||| |||||||| || || ||| | | || || |||||||||||| | |||||||| || || ||||| |||||||| |||||||||
-----------------------------------gctggaaggaagttgattggcttaaatgtatttgttttattcttg--tacaagtcactttttatattcattagtaagacactctattttatcgttattgcagTTTCATTATGCTGTGTTCTTCGCATATATGAGGTTAAGGGAACAGGAGATCAGGAACTTAATGTGGATTTCAGAATGTGTTGCTCAGAATCAGAAGTCCA--------------------------------
upper sequence: GRMZM2G372709_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G37520.1 (Glycine max), 3'ss of exon 9
gtaggtatgcatatattttgctttggtgtgttgtagcattataagaatcacttcatgctatcacagttgcactcttggagattcaaaactattctccattcat-gctatgttgatatgtctggtatgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
| | || | | | | || ||| ||| | || || || | || | | | |||||| || | || | | | | | | ||| |||| || |||| ||| |||||||| || || ||| | | || || |||||||||||| | |||||||| || || ||||| |||||||| |||||||||
-----------------------------ctggaaggaagttgattggcttttaatg-tatttgatttattcttgtgcaagtta-----tttcttatattcattagtaagatgctctattt--tgtcactattgcagTTTCATTATGCTGTGTTCTTCGCATATATGAGGTTAAGGGAACAGGAGATCAGGAACTTAATGTGGATTTCAGAATGTGTTGCTCAGAATCAGAAGTCCA--------------------------------
upper sequence: GRMZM2G372709_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G28710.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------------------------------gtaggtatgcatatattttgctttggtgt---------gttgtagc-attataagaatcacttcatg-ctatcacagttgcactcttggagattcaaaactattctccattcatgc--tatgttgata-tgtctggta-----tgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
| || || | | ||||| || ||| ||| | || || ||||| | ||| ||| | | || | | || |||| ||||||| ||| | | | || || | || | ||| ||||||| || | || ||||| ||||| || ||| | | ||||| |||||||||||||| |||||||| ||||| ||||| || |||||||||||||||
gtttgttttcctctccccaaatgaaccgcaaagaactttccaaagtccacaaaatctaggctttaatgataaccttcggttttagttgcttcaatgataacttctggactaatacattagagagtctgattgtgttatgcttctctcaattcatgtattatactaacaatggttgttcaaacctgagttttgcagTTCCATTACGCGGTATTCTTTGCGTATATGAGGTTAAGAGAGCAGGAGATCAGGAACCTTATGTGGATATCTGAATGTGTTGCACAGAACCAGAAGTCCA--------------------------------
upper sequence: GRMZM2G372709_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G28715.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------------gtaggtatgcatatattttgctttggtgtgttgtagcatt---ataaga-atcacttcatgctatcacagt---tgcactcttggagattcaaa--actatt-ctccattcatgct--atgttgata-tgtctggta-----tgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
|| || | | | | | || | | | | ||| |||||| | || ||| || ||| || | || || | | | ||| || ||| ||||| | || | | | | || || || ||| ||||||| || | || ||||| ||||| || ||| | || ||||| ||||||||||||||||||||||| ||||| ||||| || |||||||||||||||
gtttgcatccctctcccaaaatgaaccacagata-actttcctctagaactgaattttaattggattcagataagagaccatggagtgcgattacataatgtgatgtgttataggcttatataactgtttctcaattcacgtccaatactaacagtagttgttaaaacatgatatttgcagTTCCATTACGCGGTATTCTTTGCGTATATGAGGTTGCGGGAGCAGGAGATCAGGAACCTGATGTGGATATCTGAATGTGTTGCACAGAACCAGAAGTCCA--------------------------------
upper sequence: GRMZM2G372709_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv14s0108g00080.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------gtaggtatgcatatattttgctttggtgtgttgtagcattataagaatc-acttcat---gctatcacagttgcactcttggagattcaaaactattctc-cattcatgct-----atgttgatatgtctggta-----tgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
|| | ||||| || | | | || | | | ||| || ||||||| ||| | | | | || | |||| | | || | | ||| | | || || |||| | | | || ||||||| |||| ||||||||| || ||||| ||| | | ||||| ||||||||||| ||||||||||| ||||| ||||| ||||||||||||||||| |
gttagtatttcagaaacaaaacaaccaaaatttctttccaaactctgtttg-atgcacatctatggtttgtgagaacagactcatggctggacctgacttcatctagctttgatcggggttgcttttaatattctagttgactcccatactcagtttcactaacaatggaatatctgtttccctttctgagctgcagTTCCATTATGGTGTTTTCTTTGCTTACATGAGGTTGAGGGAGCAGGAGATCAGGAATCTGATGTGGATATCTGAATGTGTGGCTCAGAACCAGAAGTCTC--------------------------------
upper sequence: GRMZM2G372709_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ21507 (Selaginella moellendorffii), 3'ss of exon 9
gtaggtatgcatatattttgctttggtgtgttgtagcattataagaatcacttcatgctatcacagttgcactcttggagattcaaaactattctccattcatgctatgttgatatgtctggtatgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
| |||| | | ||| || | | | || | | | || | || |||||||||| | || || || || ||| || | || || ||||||||||||||||| || |||||||| || |||||||| || |||||||| ||| ||
--------------------------------------------------------------------------gtaactgctcaatgttgtgctc--ttaac----ttctaat-tcttagaggtgtttcctgcagTTCCACTACGCAGTGTTTTTTGCATACGTCCGACTACGGGAGCAAGAGATCAGGAATCTCATGTGGATATCAGAGTGTGTTGCACAGAACCAAAAGAACC--------------------------------
upper sequence: GRMZM2G372709_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ27108 (Selaginella moellendorffii), 3'ss of exon 9
gtaggtatgcatatattttgctttggtgtgttgtagcattataagaatcacttcatgctatcacagttgcactcttggagattcaaaactattctccattcatgctatgttgatatgtctggtatgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
| |||| | ||| || | || | || | | | || | ||||||||||||| | || || || || ||| || | || || |||||||||||||| || || |||||||| || |||||||| || |||||||| ||| ||
--------------------------------------------------------------------------gtaactgctcaatgttgcgctc--ttaa----attctaat-tcttagaggtgtttcctgtagTTCCACTACGCAGTGTTTTTTGCATACGTCCGACTACGGGAGCAAGAGATCAGAAATCTCATGTGGATATCAGAGTGTGTTGCACAGAACCAAAAGAACC-------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtctggtatgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
ttttcttcgc CT-rich tract
ttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtatgcatatattttgctttggtgtgttgtagcattataagaatcacttcatgctatcacagttgcactcttggagattcaaaactattctccattcatgctatgttgatatgtctggtatgggccttgtagttccactatgttgttttcttcgcgtacatcagGCTCCGCGAGCAAGAGATCAGGAACCTGATGTGGATCTCTGAGTGTGTCGCTCAGAACCAGAAGTCCCAGGTCCACGACAGTGTCGTGTTCATCTTCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT