Sequence
atgc intronic sequence ATGC exonic sequence...ctattagctctatccctgtggtagatatcatgtgatatgaaccacgaatagtcgacaacacaactgtactcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g32960.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------------------------------------ctattagctctatccctgtggtagatatcatgtgatatgaaccacgaatagtcgacaacacaactgtactcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
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gtcagctctccaatttctgctctaggaacccaagttcttcgtttgtctcggtggtcaaatttgtttttccttgcacactctctttatctttaatcttctcagttct--ccctacaatggatgtaatatgatgaaaaa---acatgatcccccatcgtgcttcgcttaatgttctctatctcgtgatcttatctagATGATGGAATGGTGGTATCAATCTGCTGAGGAAAGAATGTCAGCTCCGACTGTATATCCCCCACCCCCTCCTCCACCTCTGCCAAAG
upper sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 6
---ctattagctctatccctgtggtagatatcatgtga--tatgaaccacgaatagtcgacaacacaactgtactcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
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taagtatgctttctggtgatatgctgttaaataggttagctttatgtgcttattactaaggagcataattattaaca-catcacctatttgaa----ttatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
upper sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G43700.1 (Glycine max), 3'ss of exon 5
---ctattagctctatccctgtggtagatatcatgtga--tatgaaccacgaatagtcgacaacacaactgtactcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
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taagtatgccttctggtgatatgctgctaaataggttagctttatgtgccaatcactaaggagcataattattaaca-catcacctatttga--attttgt--agATGATGGAATGGTGGTACCAATCTGCTGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCTCCCCCTCCTCCGCCTCCACCAAAG
upper sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 7
---ctattagctctatc--cctgtggtagatatcatgtgatatgaaccacgaatagtcgacaacacaactgtactcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
|| | || | | | ||||||| | | || || || |||| || | | | || | ||| | | | ||| | |||||||||| |||||||||||||| |||||||| ||| | |||||||| || || || || ||||| || ||||||||| | || |||
atacttatggcgtttttgactctcggtagatttttcatcgcat-aatcatt--tagttgaacctaaacatctagctcattttcgtgtgtttttggttttgt--agATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
upper sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0036g01130.t01 (Vitis vinifera), 3'ss of exon 7
-ctattagctctatccctgtggtagatatcatgtgatatgaaccacgaatagtcgacaacacaactgtac-tcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
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ttgacatgagttataatcatggtaggattctgttcttgctgtttaacatgttttgtagatctagttttccattgacatgctattgatttgaac--tactcagATGATGGAGTGGTGGTACCAATCTGCTGAGGAAAGAATGTCAGCTCCAACTGTATACCCCCCACCACCTCCCCCTCCACCTCCAAAG
upper sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S26_47V6.1 (Physcomitrella patens), 3'ss of exon 7
ctattagctctatccctgtggtagatatcatgtgatatgaaccacgaatagtcgacaacacaactgtactcagtgttctcttt---ctgataac-tttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
|| | || | || || || ||| | | | ||| || ||| | | | | ||| | | ||| | |||||| |||| |||||||| || ||||| ||||||||| || |||| || |||| ||||| |||||||||||||| || |||| |
---ttggtggcattttagcc-tatatctccgtcttcatgcgtcctagctgttgcacatgcatgttgaactgtggactttgtggaaactggaatcgtttgtacagATGGTGGAATGGTGGTACCAGTCTGCAGAAGAAAGAGTGACAGCACCTGCTGTTTATCCTCCACCCCCTCCTCCGCCGCCTCCAGTG
upper sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ15566 (Selaginella moellendorffii), 3'ss of exon 7
ctattagctctatccctgtggtagatatcatgtgatatgaaccacgaatagtcgacaacacaactgtact-cagtgttctctttctgataactttatcc--agATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
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--------------------------------------------------gtacgcactcttctttcactgcagttccatacaactcctaacacgagcctcagATGATGGAATGGTGGTATCAATCTGCCGAGGAACGAGTCATGGCCCCTACGATATATCCCCCGCCTCCACCACCACCGCCACCAAAG
upper sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ38878 (Selaginella moellendorffii), 3'ss of exon 7
ctattagctctatccctgtggtagatatcatgtgatatgaaccacgaatagtcgacaacacaactgtact-cagtgttctctttctgataactttatcc--agATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
|| || | ||| |||| | || |||| | || |||||||||| ||||||||||||||||| || ||| || | || || || ||||||| || || || || || || | || |||
--------------------------------------------------gtacgcactctccttccactgcagttccatacaactcctaacacgagcctcagATGATGGAATGGTGGTATCAATCTGCCGAGGAACGAGTCATGGCCCCTACGATATATCCCCCGCCTCCACCACCACCGCCACCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatagtcgacaacacaactgtactcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
tgataac putative branch site (score: 2)
ctttatcc CT-rich tract
ataactttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctattagctctatccctgtggtagatatcatgtgatatgaaccacgaatagtcgacaacacaactgtactcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - -atccctg
- - - - - - - - - - - - - - catgtga
- - - - - - - - - - - - - - - - - - - gaaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caacaca
