RetrogeneDB ID: retro_hsap_3678

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:149433147..149433808(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000219487
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPB2
• Ensembl ID: ENSG00000125870
• Aliases: SNRPB2, Msl1
• Description: small nuclear ribonucleoprotein polypeptide B [Source:HGNC Symbol;Acc:11155]

Sequence

>retro_hsap_3678
ATGGATATCAGACCAAATCATACAATTTATATCAACAATATGAATGACAAAATTAAAAAGGAAGAATTGAAGAGATGCCT
ATATGCCCTGTTTTCTCAGTTTGGTCATGTGGTGGACTTTGTGGCTTTAAAGACCATGAAGATGAGGGGCAGGGCTTTGT
CATATTTAAGGAACTGGGCTCATCCACAAATGCTTAGAGACAGTCACAAGGATTTCCATTTTATGGTAAACCAATGCGAA
TACATATGCAAAAACAGATTTGGATATAATATCTGAAATGTGTGGCACTTTTGCTGACAAAGAAAAGAAAAAAGCCAAAA
CTGTGGAACAGACTGCAACAACCACAAACAAAAGGCCTGGCTAGGGAACTCCAAATTCAGCTAGTACCCAAGGAAATTCA
ACACCAAATCCTCAGGTCCTCGATTACCCTCCAAACTATATTTTATTCCTTAATAACTTACCAGAAGAGACTAATGAGAT
GATGTTATCCATGCTGTTTAATCAGTTCCCTGGCTTCAAGGAAGTATGTCTAGTACCAGGGAGGCATGACATTGCTTTTG
TTGAATTTGAAAATGATGGGAAGGCTGGAGCTGCCAGGGATGCTTTACAGGGATTTAAGATCACAACATCCCATGCTATG
AAGATCACCTATGCCAAGAAA

Alignment

ORF - retro_hsap_3678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQA-FVIFKELGSSTNALRQL
          MDIRPNHTIYINNMNDKIKKEELKR.LYALFSQFGHVVD.VALKTMKMRG.A.FVIFKELGSSTNA.RQ.
Retrocopy MDIRPNHTIYINNMNDKIKKEELKRCLYALFSQFGHVVDFVALKTMKMRGRA<FVIFKELGSSTNA*RQS

Parental  QGFPFYGKPMRIQ-YAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTATTTNKKPGQGTPNSANTQGNS
          QGFPFYGKPMRI..YAKTD.DIIS.M.GTFAD....KEKKKAKTVEQTATTTNK.PG.GTPNSA.TQGNS
Retrocopy QGFPFYGKPMRIH<YAKTDLDIISEMCGTFAD----KEKKKAKTVEQTATTTNKRPG*GTPNSASTQGNS

Parental  TPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLVPGRHDIAFVEFENDGQAGAARDALQ
          TPNPQV.DYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEV.LVPGRHDIAFVEFENDG.AGAARDALQ
Retrocopy TPNPQVLDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVCLVPGRHDIAFVEFENDGKAGAARDALQ

Parental  GFKITPSHAMKITYAKK
          GFKIT.SHAMKITYAKK
Retrocopy GFKITTSHAMKITYAKK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.00 RPM	37.27 RPM
bodymap2_adrenal	0.04 RPM	58.83 RPM
bodymap2_brain	0.00 RPM	40.18 RPM
bodymap2_breast	0.00 RPM	38.64 RPM
bodymap2_colon	0.00 RPM	54.84 RPM
bodymap2_heart	0.00 RPM	20.69 RPM
bodymap2_kidney	0.00 RPM	44.52 RPM
bodymap2_liver	0.00 RPM	19.20 RPM
bodymap2_lung	0.00 RPM	34.63 RPM
bodymap2_lymph_node	0.15 RPM	41.35 RPM
bodymap2_ovary	0.02 RPM	62.67 RPM
bodymap2_prostate	0.00 RPM	44.65 RPM
bodymap2_skeletal_muscle	0.00 RPM	23.34 RPM
bodymap2_testis	0.00 RPM	62.14 RPM
bodymap2_thyroid	0.00 RPM	57.55 RPM
bodymap2_white_blood_cells	0.37 RPM	64.93 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3678 was not detected

EST

No EST(s) were mapped for retro_hsap_3678 retrocopy.

TSS

No TSS is located nearby retro_hsap_3678 retrocopy 5' end.

Lab

retro_hsap_3678 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3678 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2492
Gorilla gorilla	retro_ggor_2487

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 118 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016500	2 retrocopies	retro_amel_235, retro_amel_490,
Bos taurus	ENSBTAG00000027506	1 retrocopy	retro_btau_1172,
Canis familiaris	ENSCAFG00000005520	4 retrocopies	retro_cfam_1097, retro_cfam_1661, retro_cfam_1689, retro_cfam_264,
Callithrix jacchus	ENSCJAG00000004811	1 retrocopy	retro_cjac_269,
Equus caballus	ENSECAG00000018407	2 retrocopies	retro_ecab_118, retro_ecab_372,
Echinops telfairi	ENSETEG00000001085	3 retrocopies	retro_etel_1283, retro_etel_1723, retro_etel_2031,
Felis catus	ENSFCAG00000026115	1 retrocopy	retro_fcat_1513,
Homo sapiens	ENSG00000125870	2 retrocopies	retro_hsap_3678 , retro_hsap_732,
Gorilla gorilla	ENSGGOG00000003937	2 retrocopies	retro_ggor_2487, retro_ggor_617,
Macropus eugenii	ENSMEUG00000016552	2 retrocopies	retro_meug_465, retro_meug_482,
Microcebus murinus	ENSMICG00000015404	1 retrocopy	retro_mmur_762,
Myotis lucifugus	ENSMLUG00000008163	5 retrocopies	retro_mluc_1450, retro_mluc_1451, retro_mluc_1452, retro_mluc_2268, retro_mluc_586,
Macaca mulatta	ENSMMUG00000014493	1 retrocopy	retro_mmul_1788,
Mus musculus	ENSMUSG00000008333	4 retrocopies	retro_mmus_1496, retro_mmus_1497, retro_mmus_2378, retro_mmus_3325,
Nomascus leucogenys	ENSNLEG00000009623	2 retrocopies	retro_nleu_477, retro_nleu_527,
Oryctolagus cuniculus	ENSOCUG00000001427	3 retrocopies	retro_ocun_1069, retro_ocun_380, retro_ocun_485,
Otolemur garnettii	ENSOGAG00000015146	1 retrocopy	retro_ogar_2042,
Ochotona princeps	ENSOPRG00000011587	2 retrocopies	retro_opri_59, retro_opri_776,
Pongo abelii	ENSPPYG00000010723	1 retrocopy	retro_pabe_630,
Pan troglodytes	ENSPTRG00000013271	2 retrocopies	retro_ptro_2492, retro_ptro_520,
Rattus norvegicus	ENSRNOG00000004967	1 retrocopy	retro_rnor_962,
Sorex araneus	ENSSARG00000002681	14 retrocopies	retro_sara_197, retro_sara_209, retro_sara_289, retro_sara_290, retro_sara_328, retro_sara_374, retro_sara_514, retro_sara_546, retro_sara_548, retro_sara_604, retro_sara_670, retro_sara_724, retro_sara_733, retro_sara_770,
Ictidomys tridecemlineatus	ENSSTOG00000009198	1 retrocopy	retro_itri_1895,
Tupaia belangeri	ENSTBEG00000012892	6 retrocopies	retro_tbel_1123, retro_tbel_2350, retro_tbel_3126, retro_tbel_3534, retro_tbel_3754, retro_tbel_530,
Tarsius syrichta	ENSTSYG00000008857	52 retrocopies	retro_tsyr_1067, retro_tsyr_1072, retro_tsyr_1083, retro_tsyr_1124, retro_tsyr_1158, retro_tsyr_1175, retro_tsyr_1216, retro_tsyr_1223, retro_tsyr_1242, retro_tsyr_1244, retro_tsyr_1245, retro_tsyr_1247, retro_tsyr_1261, retro_tsyr_1279, retro_tsyr_1323, retro_tsyr_1339, retro_tsyr_1361, retro_tsyr_1386, retro_tsyr_1434, retro_tsyr_1438, retro_tsyr_1461, retro_tsyr_1468, retro_tsyr_1469, retro_tsyr_1470, retro_tsyr_1501, retro_tsyr_1503, retro_tsyr_1513, retro_tsyr_1533, retro_tsyr_1586, retro_tsyr_1599, retro_tsyr_1616, retro_tsyr_1619, retro_tsyr_1629, retro_tsyr_1699, retro_tsyr_1720, retro_tsyr_1724, retro_tsyr_1776, retro_tsyr_1872, retro_tsyr_1930, retro_tsyr_1962, retro_tsyr_286, retro_tsyr_384, retro_tsyr_397, retro_tsyr_500, retro_tsyr_584, retro_tsyr_629, retro_tsyr_695, retro_tsyr_805, retro_tsyr_835, retro_tsyr_899, retro_tsyr_977, retro_tsyr_979,
Tursiops truncatus	ENSTTRG00000006395	1 retrocopy	retro_ttru_1545,
Vicugna pacos	ENSVPAG00000004557	1 retrocopy	retro_vpac_67,