Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttttttgcatcatttattcccatcctgtttcagtaatctttttcctcagttctagattgtttgtgagaaattgtgaattttcttagtcaaatgcattcaattgtatggccctgtatttttctgtatggctgttttggcactaatgttttgctcttttatctctttatagGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG

Basic information

species Zea mays
transcript GRMZM2G061990_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061990_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g38970.1 (Oryza sativa), 3'ss of exon 2
gtttgtttttttgcatcatttattcccatcctgtttcagtaatctttttcctcagttctagattgtttgtgagaaattgtgaattttcttagtcaaatgcattcaat--tgtatggcc--ctgtatttttctgtatggctgttttggcactaatgttttgctcttttatctc------tttat-agGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG
|||||||| |  || |||||| |  |||   | |     | |   || |   || || |    |     | |  || | ||  || ||  ||  | || |||  |||   |||||      |  |  || || |||   |  | |   ||| |||  ||  |   |||| |       ||||| |||||||||| || ||||| |||||||||||||| || |||||||| || |||||||||||||||||||| |||||||||||||||||| | || |||||||
gtttgtttct--gcttcatttgtctccactttttggtttttacaattattaacatttttgtgattcaaataaacaagtctgccttatca-agctatat-catcaaataccgtatgttttgttaaaagttcctatatttgttatctaatactgatgggttaattgcttatttgcaatgatttatcagGCTGGATATGAAACTATAATGATGAACTCCAACCCAGAGACAGTTTCAACTGACTATGATACCAGTGACCGTTTGTACTTTGAGCCATTAACGGTTGAGG

upper sequence: GRMZM2G061990_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g03360.t01 (Vitis vinifera), 3'ss of exon 2
gtttgtttttttgcatcatttattcccatcctgtttcagtaatctttttcctcagttctagattgtttgtgagaaattgtgaattttctta--gtcaaatgcattcaattg---tatggccctgtatttttctgtatggctgttttggcactaatgttttgctcttttatctctttatagGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG
                                                                           ||| ||   ||  ||    ||| ||| ||||  ||    ||| ||| | |   |   | |        |||| || |  |  |||  | | |  |  |     | || ||||| ||||| || |||||||| || |||||||||||||| ||||| || || ||||| ||||||||| | |||||||| ||  |||| ||||   
---------------------------------------------------------------------------attatggccttgtttgccatcacatggattccctttagttatagccttatgcgtacat-tgccttaaatttgtcaatt-taatttaatttctgtttgcgcagAAAGCAGGATATGAGACAATCATGATGAATTCAAATCCTGAGACAGTATCTACAGATTACGATACAAGTGATCGTCTCTACTTTGAACCGTTGACTGTTG---

upper sequence: GRMZM2G061990_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S343_21V6.1 (Physcomitrella patens), 3'ss of exon 5
gtttgtttttttgcatcatttattcccatcctgtttcagtaatctttttcctcagttctagattgtttgtgagaaattgtgaattttcttagtcaaatgcattcaattgtatggccctgtatttttctgtatggctgttttggcactaatgttttgctcttttatctctttatagGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG
||  |    |||| ||      | |  ||  | | | |           | | | ||  |   |      ||| || |  | ||||   |  | ||  | | |       || |  | | | |     ||       |  ||  | | |||     |||              | || |||||||| ||||||||||||||||| || || ||||| || |||||||| || ||||||  ||||||  | || || |||||  | ||||  |   
gtacgcgagtttgaat-----gtccaaattttatgtgatacgctgcacccgttacttaaaatataagcacgagtaaattcgtattt---tgattaatagaactatgcataatagatccgcactga---gttcaatcatgctgatagtgatgg--aactcgggagctgtgcagGATGCCGGATACGAAACTATTATGATGAACTCGAACCCAGAGACCGTATCTACTGATTACGATACCTCTGATCGACTTTATTTCGAGCCTTTAACAGCGG---

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 103

TAAGAAGAAGGTGCTGATATTGGGTGGTGGGCCAAATCGCATAGGCCAGGGCATTGAGTTTGATTACTGCTGTTGCCATGCATCATTTGCACTTCGAGAGgtttgttttt ... ctctttatagGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 109

TAAGAAGAAGGTGCTGATATTGGGTGGTGGGCCAAATCGCATAGGCCAGGGCATTGAGTTTGATTACTGCTGTTGCCATGCATCATTTGCACTTCGAGAGgtttgttttt ... ctctttatagGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

TAAGAAGAAGGTGCTGATATTGGGTGGTGGGCCAAATCGCATAGGCCAGGGCATTGAGTTTGATTACTGCTGTTGCCATGCATCATTTGCACTTCGAGAGgtttgttttt ... ctctttatagGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 52

TAAGAAGAAGGTGCTGATATTGGGTGGTGGGCCAAATCGCATAGGCCAGGGCATTGAGTTTGATTACTGCTGTTGCCATGCATCATTTGCACTTCGAGAGgtttgttttt ... ctctttatagGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttctgtatggctgttttggcactaatgttttgctcttttatctctttatagGCTGGATACGAGACTATTATGATGAACTCCAATCCTGAGACAGTCTCTACTGACTATGATACCAGTGATCGTTTGTACTTTGAGCCACTGACAGTTGAGG
                       cactaat  putative branch site (score: 52)
                             tgttttgctcttttat  CT-rich tract
                                       ttttatctctttata  TA-rich tract