Sequence
atgc intronic sequence ATGC exonic sequence...gttggtgaaaaatctggtcctgatgtttgaaatcctttgacaacccaggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g58040.2 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------------gttggtgaaaaatctggtcctgatgtttgaaatcctttg-acaacccaggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
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ctcttagtatttaagactatctgaaaacacttccaaaataaagtatattgtgtacggttgcagcaagtacttgcaatgact--agtctttcatattattcagGTTGATCCTGATGAGGTCAATGCGTTGGCACAACTAATGACATGGAAGACGGCCGTGGCTAATATTCCATATGGAGGAGCTAAAGGTGGAATAGGATGCA----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 3
------------------------------------------gttggtgaaaaatctgg--tcctgatgtttg----aaatcctttgaca----acccaggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
||||| | | | | || | | | |||| ||| | | ||||||| ||||||||||| ||||| || |||||| | ||||| ||||||||||| ||||| || ||||||||||| || |||||||| || || || |||
aacttttctgtgaaccagtccctggaactgtttatatttgtatatggtgtgtactttagattctcggttctcactctgaatcatttaatggaataaatagGTTGACCCTGATGAAGTGAATGCTTTAGCACAACTAATGACATGGAAAACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGGATAGGGTGTG----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 2
------------------------------------------gttggtgaaaaatct-ggtcctgatgtttga-----aatcctttgaca----acccaggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
||||| | | | | | || | | | | |||| ||| | | ||||||| ||||||||||| ||||| || |||||| | ||||| ||||||||||| ||||| || ||||||||||| || |||||||| || || || |||
aactttcgtttgaactagtccctggaactgtttatatttgtatatggtgtgtacttttgattctcagttctcactatgaatcatttaatggaataaatagGTTGACCCTGATGAAGTGAATGCTTTAGCACAACTAATGACATGGAAAACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGGATAGGGTGTG----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 3
----------------------------------------------gttggtgaaaaatctggtcctgatgtttgaaatcctttgacaacccaggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
| ||| || | || | | || || | ||||||| || |||||||| ||||| ||||||||| | ||||| ||||| ||||||||||| || ||||||||||| ||||||||||| || || || |||
gttatttatattctgacttacaaaaaactcagtgatttatctgtttataggttttaagttctatcactcaatcatatgtctttggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCAGTAGCGAATATACCATATGGTGGAGCCAAAGGAGGGATAGGGTGTG----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 2
------------------------------------gttggtgaaaaatctggtcctgatgtttgaaatcctttg-acaacc---------------caggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
|| |||| |||| | | | |||| | ||| | |||| ||||||| || |||||||| ||||| ||||||||| | ||||| ||||| ||||| ||||| || ||||||||||| || |||||||| ||||| || |||
caaattgaattttagctcataactgtttagtatgcttttagtgatttttctgtttataaggtttaagttccctcacacaattatgtattggcttgagtagGTTGAACCAGATGAAGTGAATGCTTTGGCACAACTAATGACATGGAAGACAGCTGTAGCAAATATACCATATGGTGGTGCCAAAGGAGGAATAGGGTGTG----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------gttggtgaaaaatctggtcctgatgtttg--aaatc---ctttgacaacc--caggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
| |||| | || | ||| | || | || | |||||||| || |||||||| || || ||||| ||| | ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| ||||| || |||
gtttgttttactctgtttttttttcatcaaaccaaaacaaattcaatattggcatgaagtaaaccagatttcggtaatcgacagGTTGAACCGGATGAAGTAAACGCTTTGGCTCAACTTATGACATGGAAAACAGCAGTGGCTAAGATACCTTATGGAGGAGCCAAAGGAGGAATCGGTTGTG----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------gttggtgaaaaatct-ggtcctgatgtttga----aatcctttgacaacc-----caggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
|| | ||| | ||| || | | ||| || | || | ||||||||||| |||||||| || || ||||| || | ||||| |||||||||||||| ||||| || || || |||||||| ||||| || ||||| |||
gtttttgaccttttgactttgaccttttgaaccaaaactcaaatgtaacaaaccagtatacaatttcggttttggtatatgatgcaaaccggttatcgttttcttgcagGTTGATCCGGATGAAGTGAACGCATTGGCTCAGCTCATGACATGGAAAACAGCAGTGGCTAAGATTCCTTACGGAGGAGCTAAAGGAGGGATTGGTTGTG----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------gttggtgaaaaatctggtcctgatgt--------ttgaaatcctttgacaaccc----aggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
| | | ||| | | || || || || || | | | | ||||||| || ||||| || ||||| ||||||||| | ||||| ||||| ||||||||||| || || ||||| || || |||||||| || || |||||||
ccagggttttcatgtagctttaaattaaatctactctccagcttgggaacagatttgtgctattgcagtttcagtttggatgatcgcatagcttttgtagGTTGACCCAGATGAGGTAAATGCTTTGGCACAACTAATGACGTGGAAGACAGCAGTAGCAAATATTCCATACGGTGGGGCCAAAGGAGGGATAGGATGTA----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S62_236V6.3 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------gttggtgaaaaatctggtcctgatgtttga---aatcc--tttgacaacc-caggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
| ||| | | | | | || | ||| | || ||| |||||||| |||| || ||||| |||||||| |||||||| |||||| | ||||| || ||||||||||| || ||||| || || || ||||||||||
gtatcttcaagtgtttgcaattagcgtaatgcacattcctttcatcgaaggtttggctggcttcctttgagttttcggtcttcaacaaaatgcgtttcgacttttgcagGTTGAGTTGAATGAGGTGAATGCTTTGGCACAGTTGATGACATGGAAATCTGCAGTGGCGAACATACCATACGGGGGAGCGAAGGGAGGCATTGGATGTA----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ36429 (Selaginella moellendorffii), 3'ss of exon 2
-----gttggtgaaaaatctggtcctg-atgtttgaaatcct--ttgacaaccc--aggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
||||| || || | | | | || | || ||| |||||| || ||||| || || | || || |||||||||||||||||||| |||||||| | ||||| ||||| ||||| || || || || ||||
gtaaaagaaacaaaaaagaaaactctatataatcgcgcttttccttatcctcctgtagGCTGATCCAGACGAAGTGAACGCACTAGCGCAGTTGATGACTTGGAAAACAGCCGTAGCTAATCTTCCATACGGAGGCGCCAAGGGAGGGATAGGCTGTA----------------------------------------------------
upper sequence: GRMZM2G178415_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ06180 (Selaginella moellendorffii), 3'ss of exon 2
-----gttggtgaaaaatctggtcctgatgtt-tgaaatcctttgacaaccc--aggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
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gtaaaagaaacaaaaaacaaaactctataatcgcgcttttccttatcctcctgtagGCTGATCCAGACGAAGTGAACGCACTAGCGCAGTTGATGACTTGGAAAACAGCCGTAGCTAATCTTCCATACGGAGGCGCCAAGGGAGGGATAGGCTGTA----------------------------------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|20300929|gb|BQ163872.1|BQ163872EST: ATGATAATGCTAGGGGACCTATGAAGGGTGGAATCAGATACCACCATGAG CAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCC
genomic: ATGATAATGCTAGGGGACCTATGAAGGGTGGAATCAGATACCACCATGAGgtaagcaaat ... tggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCC
EST:
gi|20301193|gb|BQ164136.1|BQ164136EST: ATGATAATGCTAGGGGACCTATGAAGGGTGGAATCAGATACCACCATGAG CAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCC
genomic: ATGATAATGCTAGGGGACCTATGAAGGGTGGAATCAGATACCACCATGAGgtaagcaaat ... tggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
aagttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgaaaaatctggtcctgatgtttgaaatcctttgacaacccaggttgatcctgatgaagttaatgccttggcacaattgatgacttggaaaacagCAGTAGCTAACATACCATATGGAGGAGCCAAAGGTGGAATTGGATGTAGCCCTGGAGACCTGAGCATCTCTGAGCTTGAGAGGCTTACCCGAGTTTTTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
gttggtg
- - - - - - - - - cctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attgatg