RetrogeneDB ID: retro_opri_1021

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_5863:106009..106443(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL23A
• Ensembl ID: ENSOPRG00000012620
• Aliases: None
• Description: ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]

Sequence

>retro_opri_1021
CCTGCCCCTCCCAGAGCCGGAGCCCAAGGAAGGCTCTGAAGGCCAAGAAGGTGGTGCTGAAAGGCGTCCACAGCCACAAA
AAAGATCCGCGCATCATCCACCACCCGGTGGCCCAAGACGCAGCACCTGCGCCTGCAGCCCAAATACCCTCGGAAGAGCG
CCCCCAGGAGGAACAAGCTTGACCACTATGCCATCATCAAGCTCCCCCATCACAGAGTCGGCTAGGAAGAAGACAGAAGA
CAACAACACGCTCGTGTTCATTGTGGATGTCAAGGCCAACAAGCACCAGACCAAACAAGCCATGAAGAAGCTCTAGGACA
CGGTTGTGGCCCAAGTCAACGCCCTGACCAGGCCTGATGGAGGAAAGAAGGGGTCATGTGCGCCTGGCTCCTGATGCTGA
GGCTCTGGATGCCACCAACAAAACTGGGATCATC

Alignment

ORF - retro_opri_1021 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PAPPKAEAKAKALKAKKAVLKGVHSHKKKKIRTSPTFRRPKTQRLRRQPKYPRKSAPRRNKLDHYAIIKF
          PAPP.A.A............K...S...KKIR.S.T.R.PKTQ.LR.QPKYPRKSAPRRNKLDHYAIIK.
Retrocopy PAPPRAGAQGRL*RPRRWC*KA--STATKKIRASSTTRWPKTQHLRLQPKYPRKSAPRRNKLDHYAIIKL

Parental  -PLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDG-EKKAYVRLAPDYDAL
          .P.T.ESA.KK.EDNNTLVFIVDVKANKHQ.KQA.KKL.D..VA.VN.L.RPDG.E....VRLAPD..AL
Retrocopy >PIT-ESARKKTEDNNTLVFIVDVKANKHQTKQAMKKL*DTVVAQVNALTRPDG>ERRGHVRLAPDAEAL

Parental  DVANKIGII
          D..NK.GII
Retrocopy DATNKTGII

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_1021 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 6 parental genes, and 117 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000974	10 retrocopies	retro_dord_102, retro_dord_310, retro_dord_316, retro_dord_36, retro_dord_427, retro_dord_469, retro_dord_567, retro_dord_622, retro_dord_628, retro_dord_735,
Gorilla gorilla	ENSGGOG00000016736	26 retrocopies	retro_ggor_1027, retro_ggor_1028, retro_ggor_1123, retro_ggor_120, retro_ggor_123, retro_ggor_1284, retro_ggor_140, retro_ggor_1431, retro_ggor_158, retro_ggor_1650, retro_ggor_1743, retro_ggor_1789, retro_ggor_1911, retro_ggor_1948, retro_ggor_2164, retro_ggor_2239, retro_ggor_2285, retro_ggor_229, retro_ggor_2409, retro_ggor_2475, retro_ggor_2568, retro_ggor_2764, retro_ggor_2773, retro_ggor_580, retro_ggor_611, retro_ggor_642,
Loxodonta africana	ENSLAFG00000013387	16 retrocopies	retro_lafr_1176, retro_lafr_153, retro_lafr_237, retro_lafr_33, retro_lafr_335, retro_lafr_442, retro_lafr_510, retro_lafr_525, retro_lafr_551, retro_lafr_557, retro_lafr_643, retro_lafr_78, retro_lafr_891, retro_lafr_908, retro_lafr_957, retro_lafr_96,
Monodelphis domestica	ENSMODG00000019297	3 retrocopies	retro_mdom_120, retro_mdom_870, retro_mdom_912,
Ochotona princeps	ENSOPRG00000012620	49 retrocopies	retro_opri_102, retro_opri_1021 , retro_opri_1027, retro_opri_1058, retro_opri_1153, retro_opri_1157, retro_opri_1163, retro_opri_1181, retro_opri_119, retro_opri_129, retro_opri_150, retro_opri_156, retro_opri_163, retro_opri_172, retro_opri_182, retro_opri_195, retro_opri_225, retro_opri_226, retro_opri_253, retro_opri_272, retro_opri_323, retro_opri_332, retro_opri_44, retro_opri_452, retro_opri_485, retro_opri_504, retro_opri_507, retro_opri_54, retro_opri_548, retro_opri_555, retro_opri_617, retro_opri_620, retro_opri_621, retro_opri_68, retro_opri_708, retro_opri_715, retro_opri_754, retro_opri_767, retro_opri_813, retro_opri_817, retro_opri_859, retro_opri_869, retro_opri_87, retro_opri_899, retro_opri_923, retro_opri_932, retro_opri_981, retro_opri_982, retro_opri_998,
Sarcophilus harrisii	ENSSHAG00000014549	13 retrocopies	retro_shar_188, retro_shar_373, retro_shar_407, retro_shar_448, retro_shar_498, retro_shar_564, retro_shar_624, retro_shar_630, retro_shar_685, retro_shar_698, retro_shar_824, retro_shar_829, retro_shar_835,