RetrogeneDB ID: retro_opri_703

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2496:27259..27880(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSOPRG00000007178
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_opri_703
AAAGAACCCAGGCTGGATGGCAAACTGATAGACCCGAAAAGGGCCAAAGCTCTAAAAGAGAAAGAACCCCCTAAGAAGGT
TTTTTTTTTTTAGGTGGATGGAGCCTACACACTTTGGAAGAAAAAATTAAAGAATATTTTGGAGCCTTTGGAGAGATTGA
AAACATTAAACTTCCCATGGATACAGAAACAAATCAAAGAAGAGGATTTTGTTTTATCACCAGACACAGATGAAGAACCA
GTTAAGAAATTGTTGGAAAGTGGATATCATCAAATTGGTTCTGGGAAGTGTGAAATCAAAGTGGCACAACCCAAAGAGGT
CTATAGGCAGCAGCAGCAGCAACAAAAAGGAGCAGGAGGTGCTGCGTGGGGTCATGGCCGAGGTCAGGGCCAAAACTGGA
ACCAAGGATTTAAAAACTAGTATGATCAAGGATATGGAAATTACAATAGTGCTTATGGTGGTGATCAAAACTATAGTGGC
TATGGCAGATATGAGAATATTGGGTGTAACTATGGGAACCATGGATATGGACAGGGATATGCAGGCTACAGTGGCCACCA
GAGCACTTAGGGCAAGGTATCTTGAGGGGGTGGCCATCAGCAAAACAATTACCAGTCACAC

Alignment

ORF - retro_opri_703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.91 %
• Parental protein coverage: 77.94 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEHKLDGKLID-PKRAKALKGKEPP--KKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRG
          KE..LDGKLID.P......K....P.......GG.S..T.EE.IKEYFGAFGEIENI.LPMDT.TN.RRG
Retrocopy KEPRLDGKLID<PEKGQSSKRERTP*EXXXXXGGWSLHTLEEKIKEYFGAFGEIENIKLPMDTETNQRRG

Parental  FCFITY-TDEEPVKKLLESRYHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAAGRGGVRGRGRGQGQ
          FCFIT..TDEEPVKKLLES.YHQIGSGKCEIKVAQPKEVYR...QQQ....GA.....G...G.GRGQGQ
Retrocopy FCFITR>TDEEPVKKLLESGYHQIGSGKCEIKVAQPKEVYR---QQQQQQKGAG----GAAWGHGRGQGQ

Parental  NWNQGFNNYYDQGYGNYNSAYGGDQNYSGYGGYDYTGYNYGNYGYGQGYTDYSGQQSTYGKASRGGGNHQ
          NWNQGF.N.YDQGYGNYNSAYGGDQNYSGYG.Y...G.NYGN.GYGQGY..YSG.QST.GK.S.GGG..Q
Retrocopy NWNQGFKN*YDQGYGNYNSAYGGDQNYSGYGRYENIGCNYGNHGYGQGYAGYSGHQST*GKVS*GGGHQQ

Parental  NNYQPY
          NNYQ..
Retrocopy NNYQSH

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_703 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 16 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Cavia porcellus	ENSCPOG00000015619	5 retrocopies	retro_cpor_1110, retro_cpor_1318, retro_cpor_264, retro_cpor_274, retro_cpor_567,
Equus caballus	ENSECAG00000022692	1 retrocopy	retro_ecab_1082,
Microcebus murinus	ENSMICG00000001445	4 retrocopies	retro_mmur_1016, retro_mmur_1570, retro_mmur_1572, retro_mmur_557,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ochotona princeps	ENSOPRG00000006107	10 retrocopies	retro_opri_1183, retro_opri_338, retro_opri_349, retro_opri_424, retro_opri_456, retro_opri_597, retro_opri_753, retro_opri_782, retro_opri_79, retro_opri_843,
Ochotona princeps	ENSOPRG00000007178	3 retrocopies	retro_opri_1075, retro_opri_623, retro_opri_703 ,
Ochotona princeps	ENSOPRG00000011698	2 retrocopies	retro_opri_165, retro_opri_893,
Procavia capensis	ENSPCAG00000011543	1 retrocopy	retro_pcap_366,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,
Sorex araneus	ENSSARG00000009961	1 retrocopy	retro_sara_421,