RetrogeneDB ID: retro_opri_280

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4542:859001..859447(-)
• Located in intron of: ENSOPRG00000011447

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL6
• Ensembl ID: ENSOPRG00000011800
• Aliases: None
• Description: ribosomal protein L6 [Source:HGNC Symbol;Acc:10362]

Sequence

>retro_opri_280
CAAAAAGTCCTCCAGTCAGCCTGCGAGGAAACCACTCTGATCATCCTCACCCAGTACCACAGAGATAAGAGGGCGGTTTT
CTAGAAGCTTCTGGGCAGTGGTGTGCTGCTTAAGATGAACGCTTTCTACCGAGTTGCTCTCAGTAGAACATACCAGAATT
TGTCATCACCACCTCCACGAGAATTGCTGTCAGCAGTATGAAAATCCCAAGCATCTCACTGTGCTCACTTATTGCTAGAA
GAAGCCGTTGCAGAAACCCAGGCATCATGAAGGTGAGACCTTTGACAGGCAGATGGAGAAATAGGAGATGATGGAGCAGT
AGCAAGGCTATTCAGAAAATTGTAGAACTGAAAATTTGACAGAAATCAAAGCTGTCCTCAGCTCTGGGCTACCCACGGTC
TGGTTTTGGTCTAACAAATGGAATTTATACTCACAAGTTGGTGTTC

Alignment

ORF - retro_opri_280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.06 %
• Parental protein coverage: 55.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RKLRASITPGTVLIILTGRHRGKRVVFLKQLASGLLLVTGPLSLNRVPLRRTHQ-KFVIATSTKIDISGV
          .K...S....T.LIILT..HR.KR.VF.K.L.SG.LL........RV.L.RT.Q..FVI.TST.I..S..
Retrocopy QKVLQSACEETTLIILTQYHRDKRAVF*KLLGSGVLLKMN--AFYRVALSRTYQ<EFVITTSTRIAVSSM

Parental  KL-PKHLTD-AYFKKKKLRKPRHQEGEIFDTEKEKYEITEQ-RKADQKTVDSQI-LPKIKAV-PQL-QGY
          K..PKHLT...Y..KK.L.KPRH.EGE.FD...EK.E..EQ..KA.QK.V...I.L..IKAV.PQL..GY
Retrocopy KI<PKHLTVLTYC*KKPLQKPRHHEGETFDRQMEK*EMMEQ>SKAIQKIVELKI<LTEIKAV<PQL<LGY

Parental  LRSVFALTNGVYPHKLVF
          .RS.F.LTNG.Y.HKLVF
Retrocopy PRSGFGLTNGIYTHKLVF

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_280 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.

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 107 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003060	1 retrocopy	retro_acar_171,
Bos taurus	ENSBTAG00000031723	6 retrocopies	retro_btau_1038, retro_btau_1117, retro_btau_1305, retro_btau_16, retro_btau_424, retro_btau_809,
Canis familiaris	ENSCAFG00000008873	1 retrocopy	retro_cfam_36,
Callithrix jacchus	ENSCJAG00000012450	7 retrocopies	retro_cjac_1362, retro_cjac_1620, retro_cjac_1949, retro_cjac_2723, retro_cjac_328, retro_cjac_349, retro_cjac_497,
Cavia porcellus	ENSCPOG00000013526	8 retrocopies	retro_cpor_1105, retro_cpor_1149, retro_cpor_1486, retro_cpor_382, retro_cpor_412, retro_cpor_651, retro_cpor_731, retro_cpor_982,
Equus caballus	ENSECAG00000017514	1 retrocopy	retro_ecab_811,
Felis catus	ENSFCAG00000006858	12 retrocopies	retro_fcat_1264, retro_fcat_1370, retro_fcat_1844, retro_fcat_232, retro_fcat_398, retro_fcat_500, retro_fcat_625, retro_fcat_637, retro_fcat_643, retro_fcat_690, retro_fcat_926, retro_fcat_935,
Gorilla gorilla	ENSGGOG00000003372	16 retrocopies	retro_ggor_1602, retro_ggor_1893, retro_ggor_1898, retro_ggor_2047, retro_ggor_2138, retro_ggor_236, retro_ggor_2569, retro_ggor_2597, retro_ggor_2709, retro_ggor_2745, retro_ggor_290, retro_ggor_2938, retro_ggor_356, retro_ggor_426, retro_ggor_566, retro_ggor_816,
Macaca mulatta	ENSMMUG00000007433	1 retrocopy	retro_mmul_171,
Monodelphis domestica	ENSMODG00000003096	4 retrocopies	retro_mdom_1556, retro_mdom_1624, retro_mdom_1784, retro_mdom_615,
Mustela putorius furo	ENSMPUG00000002526	9 retrocopies	retro_mputfur_1116, retro_mputfur_1279, retro_mputfur_1320, retro_mputfur_1367, retro_mputfur_1407, retro_mputfur_1445, retro_mputfur_1489, retro_mputfur_401, retro_mputfur_571,
Mus musculus	ENSMUSG00000029614	13 retrocopies	retro_mmus_1264, retro_mmus_1336, retro_mmus_1898, retro_mmus_2684, retro_mmus_276, retro_mmus_3065, retro_mmus_3579, retro_mmus_3611, retro_mmus_3622, retro_mmus_3719, retro_mmus_445, retro_mmus_465, retro_mmus_730,
Nomascus leucogenys	ENSNLEG00000027093	2 retrocopies	retro_nleu_1813, retro_nleu_43,
Oryctolagus cuniculus	ENSOCUG00000003802	5 retrocopies	retro_ocun_129, retro_ocun_17, retro_ocun_189, retro_ocun_229, retro_ocun_245,
Ochotona princeps	ENSOPRG00000011800	2 retrocopies	retro_opri_280 , retro_opri_527,
Pongo abelii	ENSPPYG00000025855	13 retrocopies	retro_pabe_1764, retro_pabe_1891, retro_pabe_2451, retro_pabe_2493, retro_pabe_2573, retro_pabe_2897, retro_pabe_3314, retro_pabe_358, retro_pabe_3677, retro_pabe_3725, retro_pabe_43, retro_pabe_472, retro_pabe_868,
Rattus norvegicus	ENSRNOG00000025936	1 retrocopy	retro_rnor_129,
Sarcophilus harrisii	ENSSHAG00000007096	2 retrocopies	retro_shar_506, retro_shar_536,
Ictidomys tridecemlineatus	ENSSTOG00000009409	3 retrocopies	retro_itri_1024, retro_itri_1125, retro_itri_684,