RetrogeneDB ID: retro_opri_1186

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_9059:5763..6195(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: UBE2B
• Ensembl ID: ENSOPRG00000006668
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2B [Source:HGNC Symbol;Acc:12473]

Sequence

>retro_opri_1186
CTCATGTGGGATTTCAAGCGATTGCAAGAGGACCCTCCTGTGGGTGTCAGTGGCGCACCCTCTGAGAACAACATCATGCA
GTGGAATGCGATTATATTTGACCCAGAAGGGACACCCTTTGAAGATGGTACTTTTAAACTAGTAATAGAATTTTCTGAAG
AATATCCAAATAAGCCACCAACTGTTAGGTTTTTATCCAAAATGTTTCATCCAAATGTGTGTGATGACGGTAGCATATGT
TTAGATATCCTTCAGAATCGATGGAGTCCAACATATGACGTATCTTCTATCTTAACATCCATTCAGTCTCTGCTGGATGA
ACCAAATCCAAACAATTCAGCCAATAGCCAGGCAGCACAGCTTTATCAGGAAAACAAACGGGAATACGAGAAGAGAGTTT
GGATCATTGTGGAGCAAAGCTGGAATGACTCT

Alignment

ORF - retro_opri_1186 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LMRDFKRLQEDPPVGVSGAPSENNIMQWNAVIFGPEGTPFEDGTFKLVIEFSEEYPNKPPTVRFLSKMFH
          LM.DFKRLQEDPPVGVSGAPSENNIMQWNA.IF.PEGTPFEDGTFKLVIEFSEEYPNKPPTVRFLSKMFH
Retrocopy LMWDFKRLQEDPPVGVSGAPSENNIMQWNAIIFDPEGTPFEDGTFKLVIEFSEEYPNKPPTVRFLSKMFH

Parental  PNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQS
          PNV..DGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPN..ANSQAAQLYQENKREYEKRV..IVEQS
Retrocopy PNVCDDGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNNSANSQAAQLYQENKREYEKRVWIIVEQS

Parental  WNDS
          WNDS
Retrocopy WNDS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_1186 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001019	2 retrocopies	retro_cfam_2099, retro_cfam_216,
Dipodomys ordii	ENSDORG00000002525	1 retrocopy	retro_dord_646,
Echinops telfairi	ENSETEG00000006522	2 retrocopies	retro_etel_1531, retro_etel_771,
Macropus eugenii	ENSMEUG00000004740	1 retrocopy	retro_meug_718,
Myotis lucifugus	ENSMLUG00000012910	4 retrocopies	retro_mluc_1319, retro_mluc_1520, retro_mluc_2216, retro_mluc_478,
Monodelphis domestica	ENSMODG00000014209	1 retrocopy	retro_mdom_1218,
Mus musculus	ENSMUSG00000020390	1 retrocopy	retro_mmus_736,
Ochotona princeps	ENSOPRG00000006668	1 retrocopy	retro_opri_1186 ,
Pteropus vampyrus	ENSPVAG00000012430	1 retrocopy	retro_pvam_141,
Sarcophilus harrisii	ENSSHAG00000016143	2 retrocopies	retro_shar_12, retro_shar_173,
Tupaia belangeri	ENSTBEG00000010294	26 retrocopies	retro_tbel_2107, retro_tbel_2133, retro_tbel_2137, retro_tbel_2157, retro_tbel_2285, retro_tbel_2286, retro_tbel_2287, retro_tbel_2288, retro_tbel_2385, retro_tbel_2616, retro_tbel_2945, retro_tbel_3251, retro_tbel_3252, retro_tbel_3253, retro_tbel_3284, retro_tbel_3878, retro_tbel_4086, retro_tbel_4087, retro_tbel_4238, retro_tbel_4289, retro_tbel_4443, retro_tbel_4585, retro_tbel_4680, retro_tbel_4684, retro_tbel_4685, retro_tbel_4693,
Tarsius syrichta	ENSTSYG00000011148	2 retrocopies	retro_tsyr_151, retro_tsyr_553,
Tursiops truncatus	ENSTTRG00000016861	1 retrocopy	retro_ttru_700,